id	sid	tid	token	lemma	pos
cord-263987-ff6kor0c	1	1	key	key	NN
cord-263987-ff6kor0c	1	2	:	:	:
cord-263987-ff6kor0c	1	3	cord-263987-ff6kor0c	cord-263987-ff6kor0c	.
cord-263987-ff6kor0c	2	1	authors	author	NNS
cord-263987-ff6kor0c	2	2	:	:	:
cord-263987-ff6kor0c	2	3	Holmes	Holmes	NNP
cord-263987-ff6kor0c	2	4	,	,	,
cord-263987-ff6kor0c	2	5	Ian	Ian	NNP
cord-263987-ff6kor0c	2	6	H.	H.	NNP
cord-263987-ff6kor0c	2	7	title	title	NN
cord-263987-ff6kor0c	2	8	:	:	:
cord-263987-ff6kor0c	2	9	Solving	solve	VBG
cord-263987-ff6kor0c	2	10	the	the	DT
cord-263987-ff6kor0c	2	11	master	master	NN
cord-263987-ff6kor0c	2	12	equation	equation	NN
cord-263987-ff6kor0c	2	13	for	for	IN
cord-263987-ff6kor0c	2	14	Indels	Indels	NNPS
cord-263987-ff6kor0c	2	15	date	date	NN
cord-263987-ff6kor0c	2	16	:	:	:
cord-263987-ff6kor0c	2	17	2017	2017	CD
cord-263987-ff6kor0c	2	18	-	-	HYPH
cord-263987-ff6kor0c	2	19	05	05	CD
cord-263987-ff6kor0c	2	20	-	-	HYPH
cord-263987-ff6kor0c	2	21	12	12	CD
cord-263987-ff6kor0c	2	22	journal	journal	NN
cord-263987-ff6kor0c	2	23	:	:	:
cord-263987-ff6kor0c	3	1	BMC	BMC	NNP
cord-263987-ff6kor0c	3	2	Bioinformatics	Bioinformatics	NNP
cord-263987-ff6kor0c	3	3	DOI	DOI	NNP
cord-263987-ff6kor0c	3	4	:	:	:
cord-263987-ff6kor0c	3	5	10.1186	10.1186	CD
cord-263987-ff6kor0c	3	6	/	/	SYM
cord-263987-ff6kor0c	3	7	s12859	s12859	CD
cord-263987-ff6kor0c	3	8	-	-	HYPH
cord-263987-ff6kor0c	3	9	017	017	CD
cord-263987-ff6kor0c	3	10	-	-	HYPH
cord-263987-ff6kor0c	3	11	1665	1665	CD
cord-263987-ff6kor0c	3	12	-	-	SYM
cord-263987-ff6kor0c	3	13	1	1	CD
cord-263987-ff6kor0c	3	14	sha	sha	NN
cord-263987-ff6kor0c	3	15	:	:	:
cord-263987-ff6kor0c	4	1	ea85420ea72fab3346afc8aaf42b17f571b99a85	ea85420ea72fab3346afc8aaf42b17f571b99a85	CD
cord-263987-ff6kor0c	4	2	doc_id	doc_id	CD
cord-263987-ff6kor0c	4	3	:	:	:
cord-263987-ff6kor0c	4	4	263987	263987	CD
cord-263987-ff6kor0c	4	5	cord_uid	cord_uid	NNS
cord-263987-ff6kor0c	4	6	:	:	:
cord-263987-ff6kor0c	4	7	ff6kor0c	ff6kor0c	JJ
cord-263987-ff6kor0c	4	8	BACKGROUND	background	NN
cord-263987-ff6kor0c	4	9	:	:	:
cord-263987-ff6kor0c	5	1	Despite	despite	IN
cord-263987-ff6kor0c	5	2	the	the	DT
cord-263987-ff6kor0c	5	3	long	long	RB
cord-263987-ff6kor0c	5	4	-	-	HYPH
cord-263987-ff6kor0c	5	5	anticipated	anticipate	VBN
cord-263987-ff6kor0c	5	6	possibility	possibility	NN
cord-263987-ff6kor0c	5	7	of	of	IN
cord-263987-ff6kor0c	5	8	putting	put	VBG
cord-263987-ff6kor0c	5	9	sequence	sequence	NN
cord-263987-ff6kor0c	5	10	alignment	alignment	NN
cord-263987-ff6kor0c	5	11	on	on	IN
cord-263987-ff6kor0c	5	12	the	the	DT
cord-263987-ff6kor0c	5	13	same	same	JJ
cord-263987-ff6kor0c	5	14	footing	footing	NN
cord-263987-ff6kor0c	5	15	as	as	IN
cord-263987-ff6kor0c	5	16	statistical	statistical	JJ
cord-263987-ff6kor0c	5	17	phylogenetics	phylogenetic	NNS
cord-263987-ff6kor0c	5	18	,	,	,
cord-263987-ff6kor0c	5	19	theorists	theorist	NNS
cord-263987-ff6kor0c	5	20	have	have	VBP
cord-263987-ff6kor0c	5	21	struggled	struggle	VBN
cord-263987-ff6kor0c	5	22	to	to	TO
cord-263987-ff6kor0c	5	23	develop	develop	VB
cord-263987-ff6kor0c	5	24	time	time	NN
cord-263987-ff6kor0c	5	25	-	-	HYPH
cord-263987-ff6kor0c	5	26	dependent	dependent	JJ
cord-263987-ff6kor0c	5	27	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	5	28	models	model	NNS
cord-263987-ff6kor0c	5	29	for	for	IN
cord-263987-ff6kor0c	5	30	indels	indel	NNS
cord-263987-ff6kor0c	5	31	that	that	WDT
cord-263987-ff6kor0c	5	32	are	be	VBP
cord-263987-ff6kor0c	5	33	as	as	RB
cord-263987-ff6kor0c	5	34	tractable	tractable	JJ
cord-263987-ff6kor0c	5	35	as	as	IN
cord-263987-ff6kor0c	5	36	the	the	DT
cord-263987-ff6kor0c	5	37	analogous	analogous	JJ
cord-263987-ff6kor0c	5	38	models	model	NNS
cord-263987-ff6kor0c	5	39	for	for	IN
cord-263987-ff6kor0c	5	40	substitution	substitution	NN
cord-263987-ff6kor0c	5	41	events	event	NNS
cord-263987-ff6kor0c	5	42	.	.	.
cord-263987-ff6kor0c	6	1	MAIN	MAIN	NNP
cord-263987-ff6kor0c	6	2	TEXT	TEXT	NNP
cord-263987-ff6kor0c	6	3	:	:	:
cord-263987-ff6kor0c	7	1	This	this	DT
cord-263987-ff6kor0c	7	2	paper	paper	NN
cord-263987-ff6kor0c	7	3	discusses	discuss	VBZ
cord-263987-ff6kor0c	7	4	progress	progress	NN
cord-263987-ff6kor0c	7	5	in	in	IN
cord-263987-ff6kor0c	7	6	the	the	DT
cord-263987-ff6kor0c	7	7	area	area	NN
cord-263987-ff6kor0c	7	8	of	of	IN
cord-263987-ff6kor0c	7	9	insertion	insertion	NN
cord-263987-ff6kor0c	7	10	-	-	HYPH
cord-263987-ff6kor0c	7	11	deletion	deletion	NN
cord-263987-ff6kor0c	7	12	models	model	NNS
cord-263987-ff6kor0c	7	13	,	,	,
cord-263987-ff6kor0c	7	14	in	in	IN
cord-263987-ff6kor0c	7	15	view	view	NN
cord-263987-ff6kor0c	7	16	of	of	IN
cord-263987-ff6kor0c	7	17	recent	recent	JJ
cord-263987-ff6kor0c	7	18	work	work	NN
cord-263987-ff6kor0c	7	19	by	by	IN
cord-263987-ff6kor0c	7	20	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	7	21	(	(	-LRB-
cord-263987-ff6kor0c	7	22	BMC	BMC	NNP
cord-263987-ff6kor0c	7	23	Bioinformatics	Bioinformatics	NNP
cord-263987-ff6kor0c	7	24	17:304	17:304	CD
cord-263987-ff6kor0c	7	25	,	,	,
cord-263987-ff6kor0c	7	26	2016	2016	CD
cord-263987-ff6kor0c	7	27	)	)	-RRB-
cord-263987-ff6kor0c	7	28	;	;	:
cord-263987-ff6kor0c	8	1	(	(	-LRB-
cord-263987-ff6kor0c	8	2	BMC	BMC	NNP
cord-263987-ff6kor0c	8	3	Bioinformatics	Bioinformatics	NNP
cord-263987-ff6kor0c	8	4	17:397	17:397	CD
cord-263987-ff6kor0c	8	5	,	,	,
cord-263987-ff6kor0c	8	6	2016	2016	CD
cord-263987-ff6kor0c	8	7	)	)	-RRB-
cord-263987-ff6kor0c	8	8	;	;	:
cord-263987-ff6kor0c	8	9	(	(	-LRB-
cord-263987-ff6kor0c	8	10	BMC	BMC	NNP
cord-263987-ff6kor0c	8	11	Bioinformatics	Bioinformatics	NNP
cord-263987-ff6kor0c	8	12	17:457	17:457	CD
cord-263987-ff6kor0c	8	13	,	,	,
cord-263987-ff6kor0c	8	14	2016	2016	CD
cord-263987-ff6kor0c	8	15	)	)	-RRB-
cord-263987-ff6kor0c	8	16	on	on	IN
cord-263987-ff6kor0c	8	17	the	the	DT
cord-263987-ff6kor0c	8	18	calculation	calculation	NN
cord-263987-ff6kor0c	8	19	of	of	IN
cord-263987-ff6kor0c	8	20	time	time	NN
cord-263987-ff6kor0c	8	21	-	-	HYPH
cord-263987-ff6kor0c	8	22	dependent	dependent	JJ
cord-263987-ff6kor0c	8	23	gap	gap	NN
cord-263987-ff6kor0c	8	24	length	length	NN
cord-263987-ff6kor0c	8	25	distributions	distribution	NNS
cord-263987-ff6kor0c	8	26	in	in	IN
cord-263987-ff6kor0c	8	27	pairwise	pairwise	JJ
cord-263987-ff6kor0c	8	28	alignments	alignment	NNS
cord-263987-ff6kor0c	8	29	,	,	,
cord-263987-ff6kor0c	8	30	and	and	CC
cord-263987-ff6kor0c	8	31	current	current	JJ
cord-263987-ff6kor0c	8	32	approaches	approach	NNS
cord-263987-ff6kor0c	8	33	for	for	IN
cord-263987-ff6kor0c	8	34	extending	extend	VBG
cord-263987-ff6kor0c	8	35	these	these	DT
cord-263987-ff6kor0c	8	36	approaches	approach	NNS
cord-263987-ff6kor0c	8	37	from	from	IN
cord-263987-ff6kor0c	8	38	ancestor	ancestor	NN
cord-263987-ff6kor0c	8	39	-	-	HYPH
cord-263987-ff6kor0c	8	40	descendant	descendant	NN
cord-263987-ff6kor0c	8	41	pairs	pair	NNS
cord-263987-ff6kor0c	8	42	to	to	TO
cord-263987-ff6kor0c	8	43	phylogenetic	phylogenetic	VB
cord-263987-ff6kor0c	8	44	trees	tree	NNS
cord-263987-ff6kor0c	8	45	.	.	.
cord-263987-ff6kor0c	9	1	CONCLUSIONS	conclusion	NNS
cord-263987-ff6kor0c	9	2	:	:	:
cord-263987-ff6kor0c	10	1	While	while	IN
cord-263987-ff6kor0c	10	2	approximations	approximation	NNS
cord-263987-ff6kor0c	10	3	that	that	WDT
cord-263987-ff6kor0c	10	4	use	use	VBP
cord-263987-ff6kor0c	10	5	finite	finite	JJ
cord-263987-ff6kor0c	10	6	-	-	HYPH
cord-263987-ff6kor0c	10	7	state	state	NN
cord-263987-ff6kor0c	10	8	machines	machine	NNS
cord-263987-ff6kor0c	10	9	(	(	-LRB-
cord-263987-ff6kor0c	10	10	Pair	Pair	NNP
cord-263987-ff6kor0c	10	11	HMMs	HMMs	NNPS
cord-263987-ff6kor0c	10	12	and	and	CC
cord-263987-ff6kor0c	10	13	transducers	transducer	NNS
cord-263987-ff6kor0c	10	14	)	)	-RRB-
cord-263987-ff6kor0c	10	15	currently	currently	RB
cord-263987-ff6kor0c	10	16	represent	represent	VBP
cord-263987-ff6kor0c	10	17	the	the	DT
cord-263987-ff6kor0c	10	18	most	most	RBS
cord-263987-ff6kor0c	10	19	practical	practical	JJ
cord-263987-ff6kor0c	10	20	approach	approach	NN
cord-263987-ff6kor0c	10	21	to	to	IN
cord-263987-ff6kor0c	10	22	problems	problem	NNS
cord-263987-ff6kor0c	10	23	such	such	JJ
cord-263987-ff6kor0c	10	24	as	as	IN
cord-263987-ff6kor0c	10	25	sequence	sequence	NN
cord-263987-ff6kor0c	10	26	alignment	alignment	NN
cord-263987-ff6kor0c	10	27	and	and	CC
cord-263987-ff6kor0c	10	28	phylogeny	phylogeny	NN
cord-263987-ff6kor0c	10	29	,	,	,
cord-263987-ff6kor0c	10	30	more	more	RBR
cord-263987-ff6kor0c	10	31	rigorous	rigorous	JJ
cord-263987-ff6kor0c	10	32	approaches	approach	NNS
cord-263987-ff6kor0c	10	33	that	that	WDT
cord-263987-ff6kor0c	10	34	work	work	VBP
cord-263987-ff6kor0c	10	35	directly	directly	RB
cord-263987-ff6kor0c	10	36	with	with	IN
cord-263987-ff6kor0c	10	37	the	the	DT
cord-263987-ff6kor0c	10	38	matrix	matrix	NN
cord-263987-ff6kor0c	10	39	exponential	exponential	NN
cord-263987-ff6kor0c	10	40	of	of	IN
cord-263987-ff6kor0c	10	41	the	the	DT
cord-263987-ff6kor0c	10	42	underlying	underlying	JJ
cord-263987-ff6kor0c	10	43	continuous	continuous	JJ
cord-263987-ff6kor0c	10	44	-	-	HYPH
cord-263987-ff6kor0c	10	45	time	time	NN
cord-263987-ff6kor0c	10	46	Markov	Markov	NNP
cord-263987-ff6kor0c	10	47	chain	chain	NN
cord-263987-ff6kor0c	10	48	also	also	RB
cord-263987-ff6kor0c	10	49	show	show	VBP
cord-263987-ff6kor0c	10	50	promise	promise	NN
cord-263987-ff6kor0c	10	51	,	,	,
cord-263987-ff6kor0c	10	52	especially	especially	RB
cord-263987-ff6kor0c	10	53	in	in	IN
cord-263987-ff6kor0c	10	54	view	view	NN
cord-263987-ff6kor0c	10	55	of	of	IN
cord-263987-ff6kor0c	10	56	recent	recent	JJ
cord-263987-ff6kor0c	10	57	advances	advance	NNS
cord-263987-ff6kor0c	10	58	.	.	.
cord-263987-ff6kor0c	11	1	Models	model	NNS
cord-263987-ff6kor0c	11	2	of	of	IN
cord-263987-ff6kor0c	11	3	sequence	sequence	NN
cord-263987-ff6kor0c	11	4	evolution	evolution	NN
cord-263987-ff6kor0c	11	5	,	,	,
cord-263987-ff6kor0c	11	6	formulated	formulate	VBN
cord-263987-ff6kor0c	11	7	as	as	IN
cord-263987-ff6kor0c	11	8	continuoustime	continuoustime	NN
cord-263987-ff6kor0c	11	9	discrete	discrete	JJ
cord-263987-ff6kor0c	11	10	-	-	HYPH
cord-263987-ff6kor0c	11	11	state	state	NN
cord-263987-ff6kor0c	11	12	Markov	Markov	NNP
cord-263987-ff6kor0c	11	13	chains	chain	NNS
cord-263987-ff6kor0c	11	14	,	,	,
cord-263987-ff6kor0c	11	15	are	be	VBP
cord-263987-ff6kor0c	11	16	central	central	JJ
cord-263987-ff6kor0c	11	17	to	to	IN
cord-263987-ff6kor0c	11	18	statistical	statistical	JJ
cord-263987-ff6kor0c	11	19	phylogenetics	phylogenetic	NNS
cord-263987-ff6kor0c	11	20	and	and	CC
cord-263987-ff6kor0c	11	21	bioinformatics	bioinformatic	NNS
cord-263987-ff6kor0c	11	22	.	.	.
cord-263987-ff6kor0c	12	1	As	as	IN
cord-263987-ff6kor0c	12	2	descriptions	description	NNS
cord-263987-ff6kor0c	12	3	of	of	IN
cord-263987-ff6kor0c	12	4	the	the	DT
cord-263987-ff6kor0c	12	5	process	process	NN
cord-263987-ff6kor0c	12	6	of	of	IN
cord-263987-ff6kor0c	12	7	nucleotide	nucleotide	JJ
cord-263987-ff6kor0c	12	8	or	or	CC
cord-263987-ff6kor0c	12	9	amino	amino	NN
cord-263987-ff6kor0c	12	10	acid	acid	NN
cord-263987-ff6kor0c	12	11	substitution	substitution	NN
cord-263987-ff6kor0c	12	12	,	,	,
cord-263987-ff6kor0c	12	13	their	-PRON-	PRP$
cord-263987-ff6kor0c	12	14	earliest	early	JJS
cord-263987-ff6kor0c	12	15	uses	use	NNS
cord-263987-ff6kor0c	12	16	were	be	VBD
cord-263987-ff6kor0c	12	17	to	to	TO
cord-263987-ff6kor0c	12	18	estimate	estimate	VB
cord-263987-ff6kor0c	12	19	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	12	20	distances	distance	NNS
cord-263987-ff6kor0c	12	21	[	[	-LRB-
cord-263987-ff6kor0c	12	22	1	1	CD
cord-263987-ff6kor0c	12	23	]	]	-RRB-
cord-263987-ff6kor0c	12	24	,	,	,
cord-263987-ff6kor0c	12	25	parameterize	parameterize	VB
cord-263987-ff6kor0c	12	26	sequence	sequence	NN
cord-263987-ff6kor0c	12	27	alignment	alignment	NN
cord-263987-ff6kor0c	12	28	algorithms	algorithm	NNS
cord-263987-ff6kor0c	12	29	[	[	-LRB-
cord-263987-ff6kor0c	12	30	2	2	CD
cord-263987-ff6kor0c	12	31	]	]	-RRB-
cord-263987-ff6kor0c	12	32	,	,	,
cord-263987-ff6kor0c	12	33	and	and	CC
cord-263987-ff6kor0c	12	34	construct	construct	VB
cord-263987-ff6kor0c	12	35	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	12	36	trees	tree	NNS
cord-263987-ff6kor0c	12	37	[	[	-LRB-
cord-263987-ff6kor0c	12	38	3	3	CD
cord-263987-ff6kor0c	12	39	]	]	-RRB-
cord-263987-ff6kor0c	12	40	.	.	.
cord-263987-ff6kor0c	13	1	Variations	variation	NNS
cord-263987-ff6kor0c	13	2	on	on	IN
cord-263987-ff6kor0c	13	3	these	these	DT
cord-263987-ff6kor0c	13	4	models	model	NNS
cord-263987-ff6kor0c	13	5	,	,	,
cord-263987-ff6kor0c	13	6	including	include	VBG
cord-263987-ff6kor0c	13	7	extra	extra	JJ
cord-263987-ff6kor0c	13	8	latent	latent	JJ
cord-263987-ff6kor0c	13	9	variables	variable	NNS
cord-263987-ff6kor0c	13	10	,	,	,
cord-263987-ff6kor0c	13	11	have	have	VBP
cord-263987-ff6kor0c	13	12	been	be	VBN
cord-263987-ff6kor0c	13	13	used	use	VBN
cord-263987-ff6kor0c	13	14	to	to	TO
cord-263987-ff6kor0c	13	15	estimate	estimate	VB
cord-263987-ff6kor0c	13	16	spatial	spatial	JJ
cord-263987-ff6kor0c	13	17	variation	variation	NN
cord-263987-ff6kor0c	13	18	in	in	IN
cord-263987-ff6kor0c	13	19	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	13	20	rates	rate	NNS
cord-263987-ff6kor0c	13	21	[	[	-LRB-
cord-263987-ff6kor0c	13	22	4	4	CD
cord-263987-ff6kor0c	13	23	,	,	,
cord-263987-ff6kor0c	13	24	5	5	CD
cord-263987-ff6kor0c	13	25	]	]	-RRB-
cord-263987-ff6kor0c	13	26	;	;	:
cord-263987-ff6kor0c	13	27	these	these	DT
cord-263987-ff6kor0c	13	28	patterns	pattern	NNS
cord-263987-ff6kor0c	13	29	of	of	IN
cord-263987-ff6kor0c	13	30	spatial	spatial	JJ
cord-263987-ff6kor0c	13	31	variation	variation	NN
cord-263987-ff6kor0c	13	32	have	have	VBP
cord-263987-ff6kor0c	13	33	been	be	VBN
cord-263987-ff6kor0c	13	34	used	use	VBN
cord-263987-ff6kor0c	13	35	to	to	TO
cord-263987-ff6kor0c	13	36	predict	predict	VB
cord-263987-ff6kor0c	13	37	exon	exon	JJ
cord-263987-ff6kor0c	13	38	structures	structure	NNS
cord-263987-ff6kor0c	13	39	of	of	IN
cord-263987-ff6kor0c	13	40	protein	protein	NN
cord-263987-ff6kor0c	13	41	-	-	HYPH
cord-263987-ff6kor0c	13	42	coding	code	VBG
cord-263987-ff6kor0c	13	43	genes	gene	NNS
cord-263987-ff6kor0c	13	44	[	[	-LRB-
cord-263987-ff6kor0c	13	45	6	6	CD
cord-263987-ff6kor0c	13	46	,	,	,
cord-263987-ff6kor0c	13	47	7	7	CD
cord-263987-ff6kor0c	13	48	]	]	-RRB-
cord-263987-ff6kor0c	13	49	,	,	,
cord-263987-ff6kor0c	13	50	foldback	foldback	NN
cord-263987-ff6kor0c	13	51	structure	structure	NN
cord-263987-ff6kor0c	13	52	of	of	IN
cord-263987-ff6kor0c	13	53	non	non	JJ
cord-263987-ff6kor0c	13	54	-	-	JJ
cord-263987-ff6kor0c	13	55	coding	code	VBG
cord-263987-ff6kor0c	13	56	RNA	RNA	NNP
cord-263987-ff6kor0c	13	57	genes	gene	NNS
cord-263987-ff6kor0c	13	58	[	[	-LRB-
cord-263987-ff6kor0c	13	59	8	8	CD
cord-263987-ff6kor0c	13	60	,	,	,
cord-263987-ff6kor0c	13	61	9	9	CD
cord-263987-ff6kor0c	13	62	]	]	-RRB-
cord-263987-ff6kor0c	13	63	,	,	,
cord-263987-ff6kor0c	13	64	regulatory	regulatory	JJ
cord-263987-ff6kor0c	13	65	elements	element	NNS
cord-263987-ff6kor0c	13	66	[	[	-LRB-
cord-263987-ff6kor0c	13	67	10	10	CD
cord-263987-ff6kor0c	13	68	]	]	-RRB-
cord-263987-ff6kor0c	13	69	,	,	,
cord-263987-ff6kor0c	13	70	ultra	ultra	JJ
cord-263987-ff6kor0c	13	71	-	-	JJ
cord-263987-ff6kor0c	13	72	conserved	conserve	VBN
cord-263987-ff6kor0c	13	73	elements	element	NNS
cord-263987-ff6kor0c	13	74	[	[	-LRB-
cord-263987-ff6kor0c	13	75	11	11	CD
cord-263987-ff6kor0c	13	76	]	]	-RRB-
cord-263987-ff6kor0c	13	77	,	,	,
cord-263987-ff6kor0c	13	78	protein	protein	NN
cord-263987-ff6kor0c	13	79	secondary	secondary	JJ
cord-263987-ff6kor0c	13	80	structures	structure	NNS
cord-263987-ff6kor0c	13	81	[	[	-LRB-
cord-263987-ff6kor0c	13	82	12	12	CD
cord-263987-ff6kor0c	13	83	]	]	-RRB-
cord-263987-ff6kor0c	13	84	,	,	,
cord-263987-ff6kor0c	13	85	and	and	CC
cord-263987-ff6kor0c	13	86	transmembrane	transmembrane	NN
cord-263987-ff6kor0c	13	87	structures	structure	NNS
cord-263987-ff6kor0c	13	88	[	[	-LRB-
cord-263987-ff6kor0c	13	89	13	13	CD
cord-263987-ff6kor0c	13	90	]	]	-RRB-
cord-263987-ff6kor0c	13	91	.	.	.
cord-263987-ff6kor0c	14	1	They	-PRON-	PRP
cord-263987-ff6kor0c	14	2	are	be	VBP
cord-263987-ff6kor0c	14	3	widely	widely	RB
cord-263987-ff6kor0c	14	4	used	use	VBN
cord-263987-ff6kor0c	14	5	to	to	TO
cord-263987-ff6kor0c	14	6	reconstruct	reconstruct	VB
cord-263987-ff6kor0c	14	7	ancestral	ancestral	JJ
cord-263987-ff6kor0c	14	8	sequences	sequence	NNS
cord-263987-ff6kor0c	14	9	[	[	-LRB-
cord-263987-ff6kor0c	14	10	14	14	CD
cord-263987-ff6kor0c	14	11	]	]	-RRB-
cord-263987-ff6kor0c	14	12	[	[	-LRB-
cord-263987-ff6kor0c	14	13	15	15	CD
cord-263987-ff6kor0c	14	14	]	]	-RRB-
cord-263987-ff6kor0c	14	15	[	[	-LRB-
cord-263987-ff6kor0c	14	16	16	16	CD
cord-263987-ff6kor0c	14	17	]	]	-RRB-
cord-263987-ff6kor0c	15	1	[	[	-LRB-
cord-263987-ff6kor0c	15	2	17	17	CD
cord-263987-ff6kor0c	15	3	]	]	-RRB-
cord-263987-ff6kor0c	15	4	[	[	-LRB-
cord-263987-ff6kor0c	15	5	18	18	CD
cord-263987-ff6kor0c	15	6	]	]	-RRB-
cord-263987-ff6kor0c	15	7	[	[	-LRB-
cord-263987-ff6kor0c	15	8	19	19	CD
cord-263987-ff6kor0c	15	9	]	]	-RRB-
cord-263987-ff6kor0c	16	1	[	[	-LRB-
cord-263987-ff6kor0c	16	2	20	20	CD
cord-263987-ff6kor0c	16	3	]	]	-RRB-
cord-263987-ff6kor0c	16	4	[	[	-LRB-
cord-263987-ff6kor0c	16	5	21	21	CD
cord-263987-ff6kor0c	16	6	]	]	-RRB-
cord-263987-ff6kor0c	17	1	[	[	-LRB-
cord-263987-ff6kor0c	17	2	22	22	CD
cord-263987-ff6kor0c	17	3	]	]	-RRB-
cord-263987-ff6kor0c	17	4	,	,	,
cord-263987-ff6kor0c	17	5	a	a	DT
cord-263987-ff6kor0c	17	6	method	method	NN
cord-263987-ff6kor0c	17	7	that	that	WDT
cord-263987-ff6kor0c	17	8	is	be	VBZ
cord-263987-ff6kor0c	17	9	finding	find	VBG
cord-263987-ff6kor0c	17	10	increasing	increase	VBG
cord-263987-ff6kor0c	17	11	application	application	NN
cord-263987-ff6kor0c	17	12	in	in	IN
cord-263987-ff6kor0c	17	13	synthetic	synthetic	JJ
cord-263987-ff6kor0c	17	14	biology	biology	NN
cord-263987-ff6kor0c	17	15	[	[	-LRB-
cord-263987-ff6kor0c	17	16	16	16	CD
cord-263987-ff6kor0c	17	17	,	,	,
cord-263987-ff6kor0c	17	18	[	[	-LRB-
cord-263987-ff6kor0c	17	19	20	20	CD
cord-263987-ff6kor0c	17	20	]	]	-RRB-
cord-263987-ff6kor0c	17	21	[	[	-LRB-
cord-263987-ff6kor0c	17	22	21	21	CD
cord-263987-ff6kor0c	17	23	]	]	-RRB-
cord-263987-ff6kor0c	17	24	[	[	-LRB-
cord-263987-ff6kor0c	17	25	22	22	CD
cord-263987-ff6kor0c	17	26	]	]	-RRB-
cord-263987-ff6kor0c	17	27	.	.	.
cord-263987-ff6kor0c	18	1	Trees	tree	NNS
cord-263987-ff6kor0c	18	2	built	build	VBD
cord-263987-ff6kor0c	18	3	using	use	VBG
cord-263987-ff6kor0c	18	4	substitution	substitution	NN
cord-263987-ff6kor0c	18	5	models	model	NNS
cord-263987-ff6kor0c	18	6	used	use	VBN
cord-263987-ff6kor0c	18	7	to	to	TO
cord-263987-ff6kor0c	18	8	classify	classify	VB
cord-263987-ff6kor0c	18	9	species	specie	NNS
cord-263987-ff6kor0c	18	10	[	[	-LRB-
cord-263987-ff6kor0c	18	11	23	23	CD
cord-263987-ff6kor0c	18	12	]	]	-RRB-
cord-263987-ff6kor0c	18	13	,	,	,
cord-263987-ff6kor0c	18	14	predict	predict	VBP
cord-263987-ff6kor0c	18	15	protein	protein	NN
cord-263987-ff6kor0c	18	16	function	function	NN
cord-263987-ff6kor0c	18	17	[	[	-LRB-
cord-263987-ff6kor0c	18	18	24	24	CD
cord-263987-ff6kor0c	18	19	]	]	-RRB-
cord-263987-ff6kor0c	18	20	,	,	,
cord-263987-ff6kor0c	18	21	inform	inform	VB
cord-263987-ff6kor0c	18	22	conservation	conservation	NN
cord-263987-ff6kor0c	18	23	efforts	effort	NNS
cord-263987-ff6kor0c	18	24	[	[	-LRB-
cord-263987-ff6kor0c	18	25	25	25	CD
cord-263987-ff6kor0c	18	26	]	]	-RRB-
cord-263987-ff6kor0c	18	27	,	,	,
cord-263987-ff6kor0c	18	28	or	or	CC
cord-263987-ff6kor0c	18	29	identify	identify	VB
cord-263987-ff6kor0c	18	30	novel	novel	JJ
cord-263987-ff6kor0c	18	31	pathogens	pathogen	NNS
cord-263987-ff6kor0c	18	32	[	[	-LRB-
cord-263987-ff6kor0c	18	33	26	26	CD
cord-263987-ff6kor0c	18	34	]	]	-RRB-
cord-263987-ff6kor0c	18	35	.	.	.
cord-263987-ff6kor0c	19	1	In	in	IN
cord-263987-ff6kor0c	19	2	the	the	DT
cord-263987-ff6kor0c	19	3	analysis	analysis	NN
cord-263987-ff6kor0c	19	4	of	of	IN
cord-263987-ff6kor0c	19	5	rapidly	rapidly	RB
cord-263987-ff6kor0c	19	6	evolving	evolve	VBG
cord-263987-ff6kor0c	19	7	pathogens	pathogen	NNS
cord-263987-ff6kor0c	19	8	,	,	,
cord-263987-ff6kor0c	19	9	these	these	DT
cord-263987-ff6kor0c	19	10	methods	method	NNS
cord-263987-ff6kor0c	19	11	are	be	VBP
cord-263987-ff6kor0c	19	12	used	use	VBN
cord-263987-ff6kor0c	19	13	to	to	TO
cord-263987-ff6kor0c	19	14	uncover	uncover	VB
cord-263987-ff6kor0c	19	15	population	population	NN
cord-263987-ff6kor0c	19	16	histories	history	NNS
cord-263987-ff6kor0c	19	17	[	[	-LRB-
cord-263987-ff6kor0c	19	18	27	27	CD
cord-263987-ff6kor0c	19	19	]	]	-RRB-
cord-263987-ff6kor0c	19	20	,	,	,
cord-263987-ff6kor0c	19	21	analyze	analyze	VB
cord-263987-ff6kor0c	19	22	Correspondence	correspondence	NN
cord-263987-ff6kor0c	19	23	:	:	:
cord-263987-ff6kor0c	20	1	ihh@berkeley.edu	ihh@berkeley.edu	NNP
cord-263987-ff6kor0c	20	2	Dept	Dept	NNP
cord-263987-ff6kor0c	20	3	of	of	IN
cord-263987-ff6kor0c	20	4	Bioengineering	Bioengineering	NNP
cord-263987-ff6kor0c	20	5	,	,	,
cord-263987-ff6kor0c	20	6	University	University	NNP
cord-263987-ff6kor0c	20	7	of	of	IN
cord-263987-ff6kor0c	20	8	California	California	NNP
cord-263987-ff6kor0c	20	9	,	,	,
cord-263987-ff6kor0c	20	10	94720	94720	CD
cord-263987-ff6kor0c	20	11	Berkeley	Berkeley	NNP
cord-263987-ff6kor0c	20	12	,	,	,
cord-263987-ff6kor0c	20	13	USA	USA	NNP
cord-263987-ff6kor0c	20	14	transmission	transmission	NN
cord-263987-ff6kor0c	20	15	dynamics	dynamic	NNS
cord-263987-ff6kor0c	20	16	[	[	-LRB-
cord-263987-ff6kor0c	20	17	28	28	CD
cord-263987-ff6kor0c	20	18	]	]	-RRB-
cord-263987-ff6kor0c	20	19	,	,	,
cord-263987-ff6kor0c	20	20	reconstruct	reconstruct	VB
cord-263987-ff6kor0c	20	21	key	key	JJ
cord-263987-ff6kor0c	20	22	transmission	transmission	NN
cord-263987-ff6kor0c	20	23	events	event	NNS
cord-263987-ff6kor0c	20	24	[	[	-LRB-
cord-263987-ff6kor0c	20	25	29	29	CD
cord-263987-ff6kor0c	20	26	]	]	-RRB-
cord-263987-ff6kor0c	20	27	,	,	,
cord-263987-ff6kor0c	20	28	and	and	CC
cord-263987-ff6kor0c	20	29	predict	predict	VB
cord-263987-ff6kor0c	20	30	future	future	JJ
cord-263987-ff6kor0c	20	31	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	20	32	trends	trend	NNS
cord-263987-ff6kor0c	20	33	[	[	-LRB-
cord-263987-ff6kor0c	20	34	30	30	CD
cord-263987-ff6kor0c	20	35	]	]	-RRB-
cord-263987-ff6kor0c	20	36	.	.	.
cord-263987-ff6kor0c	21	1	There	there	EX
cord-263987-ff6kor0c	21	2	are	be	VBP
cord-263987-ff6kor0c	21	3	many	many	JJ
cord-263987-ff6kor0c	21	4	other	other	JJ
cord-263987-ff6kor0c	21	5	applications	application	NNS
cord-263987-ff6kor0c	21	6	;	;	:
cord-263987-ff6kor0c	21	7	the	the	DT
cord-263987-ff6kor0c	21	8	ones	one	NNS
cord-263987-ff6kor0c	21	9	listed	list	VBN
cord-263987-ff6kor0c	21	10	above	above	RB
cord-263987-ff6kor0c	21	11	were	be	VBD
cord-263987-ff6kor0c	21	12	selected	select	VBN
cord-263987-ff6kor0c	21	13	to	to	TO
cord-263987-ff6kor0c	21	14	give	give	VB
cord-263987-ff6kor0c	21	15	some	some	DT
cord-263987-ff6kor0c	21	16	idea	idea	NN
cord-263987-ff6kor0c	21	17	of	of	IN
cord-263987-ff6kor0c	21	18	how	how	WRB
cord-263987-ff6kor0c	21	19	influential	influential	JJ
cord-263987-ff6kor0c	21	20	these	these	DT
cord-263987-ff6kor0c	21	21	models	model	NNS
cord-263987-ff6kor0c	21	22	have	have	VBP
cord-263987-ff6kor0c	21	23	been	be	VBN
cord-263987-ff6kor0c	21	24	.	.	.
cord-263987-ff6kor0c	22	1	Continuous	continuous	JJ
cord-263987-ff6kor0c	22	2	-	-	HYPH
cord-263987-ff6kor0c	22	3	time	time	NN
cord-263987-ff6kor0c	22	4	Markov	Markov	NNP
cord-263987-ff6kor0c	22	5	chains	chain	NNS
cord-263987-ff6kor0c	22	6	describe	describe	VBP
cord-263987-ff6kor0c	22	7	evolution	evolution	NN
cord-263987-ff6kor0c	22	8	in	in	IN
cord-263987-ff6kor0c	22	9	a	a	DT
cord-263987-ff6kor0c	22	10	state	state	NN
cord-263987-ff6kor0c	22	11	space	space	NN
cord-263987-ff6kor0c	22	12	,	,	,
cord-263987-ff6kor0c	22	13	for	for	IN
cord-263987-ff6kor0c	22	14	example	example	NN
cord-263987-ff6kor0c	22	15	the	the	DT
cord-263987-ff6kor0c	22	16	set	set	NN
cord-263987-ff6kor0c	22	17	of	of	IN
cord-263987-ff6kor0c	22	18	nucleotides	nucleotide	NNS
cord-263987-ff6kor0c	22	19	=	=	NFP
cord-263987-ff6kor0c	22	20	{	{	-LRB-
cord-263987-ff6kor0c	22	21	A	A	NNP
cord-263987-ff6kor0c	22	22	,	,	,
cord-263987-ff6kor0c	22	23	C	C	NNP
cord-263987-ff6kor0c	22	24	,	,	,
cord-263987-ff6kor0c	22	25	G	G	NNP
cord-263987-ff6kor0c	22	26	,	,	,
cord-263987-ff6kor0c	22	27	T	T	NNP
cord-263987-ff6kor0c	22	28	}	}	-RRB-
cord-263987-ff6kor0c	22	29	.	.	.
cord-263987-ff6kor0c	23	1	The	the	DT
cord-263987-ff6kor0c	23	2	stochastic	stochastic	JJ
cord-263987-ff6kor0c	23	3	process	process	NN
cord-263987-ff6kor0c	23	4	φ(t	φ(t	CD
cord-263987-ff6kor0c	23	5	)	)	-RRB-
cord-263987-ff6kor0c	23	6	at	at	IN
cord-263987-ff6kor0c	23	7	any	any	DT
cord-263987-ff6kor0c	23	8	given	give	VBN
cord-263987-ff6kor0c	23	9	instant	instant	NN
cord-263987-ff6kor0c	23	10	of	of	IN
cord-263987-ff6kor0c	23	11	time	time	NN
cord-263987-ff6kor0c	23	12	,	,	,
cord-263987-ff6kor0c	23	13	t	t	NNP
cord-263987-ff6kor0c	23	14	,	,	,
cord-263987-ff6kor0c	23	15	takes	take	VBZ
cord-263987-ff6kor0c	23	16	one	one	CD
cord-263987-ff6kor0c	23	17	of	of	IN
cord-263987-ff6kor0c	23	18	the	the	DT
cord-263987-ff6kor0c	23	19	values	value	NNS
cord-263987-ff6kor0c	23	20	in	in	RP
cord-263987-ff6kor0c	23	21	.	.	.
cord-263987-ff6kor0c	24	1	Let	let	VB
cord-263987-ff6kor0c	24	2	p(t	p(t	NNS
cord-263987-ff6kor0c	24	3	)	)	-RRB-
cord-263987-ff6kor0c	24	4	be	be	VB
cord-263987-ff6kor0c	24	5	a	a	DT
cord-263987-ff6kor0c	24	6	vector	vector	NN
cord-263987-ff6kor0c	24	7	describing	describe	VBG
cord-263987-ff6kor0c	24	8	the	the	DT
cord-263987-ff6kor0c	24	9	marginal	marginal	JJ
cord-263987-ff6kor0c	24	10	probability	probability	NN
cord-263987-ff6kor0c	24	11	distribution	distribution	NN
cord-263987-ff6kor0c	24	12	of	of	IN
cord-263987-ff6kor0c	24	13	the	the	DT
cord-263987-ff6kor0c	24	14	process	process	NN
cord-263987-ff6kor0c	24	15	at	at	IN
cord-263987-ff6kor0c	24	16	a	a	DT
cord-263987-ff6kor0c	24	17	single	single	JJ
cord-263987-ff6kor0c	24	18	point	point	NN
cord-263987-ff6kor0c	24	19	in	in	IN
cord-263987-ff6kor0c	24	20	time	time	NN
cord-263987-ff6kor0c	24	21	:	:	:
cord-263987-ff6kor0c	24	22	p	p	NN
cord-263987-ff6kor0c	24	23	i	i	PRP
cord-263987-ff6kor0c	24	24	(	(	-LRB-
cord-263987-ff6kor0c	24	25	t	t	NN
cord-263987-ff6kor0c	24	26	)	)	-RRB-
cord-263987-ff6kor0c	24	27	=	=	NFP
cord-263987-ff6kor0c	25	1	P(φ(t	P(φ(t	NNP
cord-263987-ff6kor0c	25	2	)	)	-RRB-
cord-263987-ff6kor0c	25	3	=	=	NFP
cord-263987-ff6kor0c	26	1	i	i	PRP
cord-263987-ff6kor0c	26	2	)	)	-RRB-
cord-263987-ff6kor0c	26	3	.	.	.
cord-263987-ff6kor0c	27	1	The	the	DT
cord-263987-ff6kor0c	27	2	time	time	NN
cord-263987-ff6kor0c	27	3	-	-	HYPH
cord-263987-ff6kor0c	27	4	evolution	evolution	NN
cord-263987-ff6kor0c	27	5	of	of	IN
cord-263987-ff6kor0c	27	6	this	this	DT
cord-263987-ff6kor0c	27	7	vector	vector	NN
cord-263987-ff6kor0c	27	8	is	be	VBZ
cord-263987-ff6kor0c	27	9	governed	govern	VBN
cord-263987-ff6kor0c	27	10	by	by	IN
cord-263987-ff6kor0c	27	11	a	a	DT
cord-263987-ff6kor0c	27	12	master	master	NN
cord-263987-ff6kor0c	27	13	equation	equation	NN
cord-263987-ff6kor0c	27	14	where	where	WRB
cord-263987-ff6kor0c	27	15	,	,	,
cord-263987-ff6kor0c	27	16	for	for	IN
cord-263987-ff6kor0c	27	17	i	i	PRP
cord-263987-ff6kor0c	27	18	,	,	,
cord-263987-ff6kor0c	27	19	j	j	NNP
cord-263987-ff6kor0c	27	20	∈	∈	NNP
cord-263987-ff6kor0c	27	21	and	and	CC
cord-263987-ff6kor0c	27	22	i	i	NN
cord-263987-ff6kor0c	27	23	=	=	SYM
cord-263987-ff6kor0c	27	24	j	j	NNP
cord-263987-ff6kor0c	27	25	,	,	,
cord-263987-ff6kor0c	27	26	R	R	NNP
cord-263987-ff6kor0c	27	27	i	i	NNP
cord-263987-ff6kor0c	27	28	,	,	,
cord-263987-ff6kor0c	27	29	j	j	NNP
cord-263987-ff6kor0c	27	30	is	be	VBZ
cord-263987-ff6kor0c	27	31	the	the	DT
cord-263987-ff6kor0c	27	32	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	27	33	rate	rate	NN
cord-263987-ff6kor0c	27	34	of	of	IN
cord-263987-ff6kor0c	27	35	mutation	mutation	NN
cord-263987-ff6kor0c	27	36	from	from	IN
cord-263987-ff6kor0c	27	37	state	state	NN
cord-263987-ff6kor0c	27	38	i	i	PRP
cord-263987-ff6kor0c	27	39	to	to	TO
cord-263987-ff6kor0c	27	40	state	state	VB
cord-263987-ff6kor0c	27	41	j.	j.	NNP
cord-263987-ff6kor0c	28	1	For	for	IN
cord-263987-ff6kor0c	28	2	probabilistic	probabilistic	JJ
cord-263987-ff6kor0c	28	3	normalization	normalization	NN
cord-263987-ff6kor0c	28	4	of	of	IN
cord-263987-ff6kor0c	28	5	Eq	Eq	NNP
cord-263987-ff6kor0c	28	6	.	.	.
cord-263987-ff6kor0c	29	1	1	1	LS
cord-263987-ff6kor0c	29	2	,	,	,
cord-263987-ff6kor0c	29	3	it	-PRON-	PRP
cord-263987-ff6kor0c	29	4	is	be	VBZ
cord-263987-ff6kor0c	29	5	then	then	RB
cord-263987-ff6kor0c	29	6	required	require	VBN
cord-263987-ff6kor0c	29	7	that	that	IN
cord-263987-ff6kor0c	29	8	The	the	DT
cord-263987-ff6kor0c	29	9	general	general	JJ
cord-263987-ff6kor0c	29	10	solution	solution	NN
cord-263987-ff6kor0c	29	11	to	to	IN
cord-263987-ff6kor0c	29	12	Eq	Eq	NNP
cord-263987-ff6kor0c	29	13	.	.	.
cord-263987-ff6kor0c	30	1	1	1	LS
cord-263987-ff6kor0c	30	2	can	can	MD
cord-263987-ff6kor0c	30	3	be	be	VB
cord-263987-ff6kor0c	30	4	written	write	VBN
cord-263987-ff6kor0c	30	5	p(t	p(t	NNS
cord-263987-ff6kor0c	30	6	)	)	-RRB-
cord-263987-ff6kor0c	30	7	=	=	NFP
cord-263987-ff6kor0c	31	1	p(0)M(t	p(0)M(t	NNP
cord-263987-ff6kor0c	31	2	)	)	-RRB-
cord-263987-ff6kor0c	31	3	where	where	WRB
cord-263987-ff6kor0c	31	4	M(t	M(t	NNP
cord-263987-ff6kor0c	31	5	)	)	-RRB-
cord-263987-ff6kor0c	31	6	is	be	VBZ
cord-263987-ff6kor0c	31	7	the	the	DT
cord-263987-ff6kor0c	31	8	matrix	matrix	NN
cord-263987-ff6kor0c	31	9	exponential	exponential	JJ
cord-263987-ff6kor0c	31	10	M(t	m(t	NN
cord-263987-ff6kor0c	31	11	)	)	-RRB-
cord-263987-ff6kor0c	32	1	=	=	NFP
cord-263987-ff6kor0c	33	1	exp(Rt	exp(Rt	NNP
cord-263987-ff6kor0c	33	2	)	)	-RRB-
cord-263987-ff6kor0c	33	3	(	(	-LRB-
cord-263987-ff6kor0c	33	4	2	2	LS
cord-263987-ff6kor0c	33	5	)	)	-RRB-
cord-263987-ff6kor0c	34	1	Entry	Entry	NNP
cord-263987-ff6kor0c	34	2	M	M	NNP
cord-263987-ff6kor0c	34	3	i	i	NNP
cord-263987-ff6kor0c	34	4	,	,	,
cord-263987-ff6kor0c	34	5	j	j	NNP
cord-263987-ff6kor0c	34	6	(	(	-LRB-
cord-263987-ff6kor0c	34	7	t	t	NNP
cord-263987-ff6kor0c	34	8	)	)	-RRB-
cord-263987-ff6kor0c	34	9	of	of	IN
cord-263987-ff6kor0c	34	10	this	this	DT
cord-263987-ff6kor0c	34	11	matrix	matrix	NN
cord-263987-ff6kor0c	34	12	is	be	VBZ
cord-263987-ff6kor0c	34	13	the	the	DT
cord-263987-ff6kor0c	34	14	probability	probability	NN
cord-263987-ff6kor0c	34	15	P(φ(t	p(φ(t	NN
cord-263987-ff6kor0c	34	16	)	)	-RRB-
cord-263987-ff6kor0c	35	1	=	=	NFP
cord-263987-ff6kor0c	36	1	j|φ(0	j|φ(0	NNP
cord-263987-ff6kor0c	36	2	)	)	-RRB-
cord-263987-ff6kor0c	37	1	=	=	NFP
cord-263987-ff6kor0c	38	1	i	i	PRP
cord-263987-ff6kor0c	38	2	)	)	-RRB-
cord-263987-ff6kor0c	38	3	that	that	IN
cord-263987-ff6kor0c	38	4	,	,	,
cord-263987-ff6kor0c	38	5	conditional	conditional	JJ
cord-263987-ff6kor0c	38	6	on	on	IN
cord-263987-ff6kor0c	38	7	starting	start	VBG
cord-263987-ff6kor0c	38	8	in	in	IN
cord-263987-ff6kor0c	38	9	state	state	NN
cord-263987-ff6kor0c	39	1	i	i	PRP
cord-263987-ff6kor0c	39	2	,	,	,
cord-263987-ff6kor0c	39	3	the	the	DT
cord-263987-ff6kor0c	39	4	system	system	NN
cord-263987-ff6kor0c	39	5	will	will	MD
cord-263987-ff6kor0c	39	6	after	after	IN
cord-263987-ff6kor0c	39	7	time	time	NN
cord-263987-ff6kor0c	39	8	t	t	NNP
cord-263987-ff6kor0c	39	9	be	be	VB
cord-263987-ff6kor0c	39	10	in	in	IN
cord-263987-ff6kor0c	39	11	state	state	NN
cord-263987-ff6kor0c	40	1	j.	j.	NNP
cord-263987-ff6kor0c	40	2	It	-PRON-	PRP
cord-263987-ff6kor0c	40	3	follows	follow	VBZ
cord-263987-ff6kor0c	40	4	,	,	,
cord-263987-ff6kor0c	40	5	by	by	IN
cord-263987-ff6kor0c	40	6	definition	definition	NN
cord-263987-ff6kor0c	40	7	,	,	,
cord-263987-ff6kor0c	40	8	that	that	IN
cord-263987-ff6kor0c	40	9	this	this	DT
cord-263987-ff6kor0c	40	10	matrix	matrix	NN
cord-263987-ff6kor0c	40	11	satisfies	satisfy	VBZ
cord-263987-ff6kor0c	40	12	the	the	DT
cord-263987-ff6kor0c	40	13	Chapman	Chapman	NNP
cord-263987-ff6kor0c	40	14	-	-	HYPH
cord-263987-ff6kor0c	40	15	Kolmogorov	Kolmogorov	NNP
cord-263987-ff6kor0c	40	16	forward	forward	RB
cord-263987-ff6kor0c	40	17	equation	equation	NN
cord-263987-ff6kor0c	40	18	:	:	:
cord-263987-ff6kor0c	40	19	That	that	DT
cord-263987-ff6kor0c	40	20	is	is	RB
cord-263987-ff6kor0c	40	21	,	,	,
cord-263987-ff6kor0c	40	22	if	if	IN
cord-263987-ff6kor0c	40	23	M	M	NNP
cord-263987-ff6kor0c	40	24	i	i	NNP
cord-263987-ff6kor0c	40	25	,	,	,
cord-263987-ff6kor0c	40	26	j	j	NNP
cord-263987-ff6kor0c	40	27	(	(	-LRB-
cord-263987-ff6kor0c	40	28	t	t	NNP
cord-263987-ff6kor0c	40	29	)	)	-RRB-
cord-263987-ff6kor0c	40	30	is	be	VBZ
cord-263987-ff6kor0c	40	31	the	the	DT
cord-263987-ff6kor0c	40	32	probability	probability	NN
cord-263987-ff6kor0c	40	33	that	that	WDT
cord-263987-ff6kor0c	40	34	state	state	NN
cord-263987-ff6kor0c	40	35	i	i	PRP
cord-263987-ff6kor0c	40	36	will	will	MD
cord-263987-ff6kor0c	40	37	,	,	,
cord-263987-ff6kor0c	40	38	after	after	IN
cord-263987-ff6kor0c	40	39	a	a	DT
cord-263987-ff6kor0c	40	40	finite	finite	JJ
cord-263987-ff6kor0c	40	41	time	time	NN
cord-263987-ff6kor0c	40	42	interval	interval	NN
cord-263987-ff6kor0c	40	43	t	t	NN
cord-263987-ff6kor0c	40	44	,	,	,
cord-263987-ff6kor0c	40	45	have	have	VBP
cord-263987-ff6kor0c	40	46	evolved	evolve	VBN
cord-263987-ff6kor0c	40	47	into	into	IN
cord-263987-ff6kor0c	40	48	state	state	NN
cord-263987-ff6kor0c	40	49	j	j	NNP
cord-263987-ff6kor0c	40	50	,	,	,
cord-263987-ff6kor0c	40	51	and	and	CC
cord-263987-ff6kor0c	40	52	M	M	NNP
cord-263987-ff6kor0c	40	53	j	j	NNP
cord-263987-ff6kor0c	40	54	,	,	,
cord-263987-ff6kor0c	40	55	k	k	NNP
cord-263987-ff6kor0c	40	56	(	(	-LRB-
cord-263987-ff6kor0c	40	57	u	u	NNP
cord-263987-ff6kor0c	40	58	)	)	-RRB-
cord-263987-ff6kor0c	40	59	is	be	VBZ
cord-263987-ff6kor0c	40	60	the	the	DT
cord-263987-ff6kor0c	40	61	analogous	analogous	JJ
cord-263987-ff6kor0c	40	62	probability	probability	NN
cord-263987-ff6kor0c	40	63	that	that	WDT
cord-263987-ff6kor0c	40	64	state	state	NN
cord-263987-ff6kor0c	40	65	j	j	NNP
cord-263987-ff6kor0c	40	66	will	will	MD
cord-263987-ff6kor0c	40	67	after	after	IN
cord-263987-ff6kor0c	40	68	time	time	NN
cord-263987-ff6kor0c	40	69	u	u	PRP
cord-263987-ff6kor0c	40	70	evolve	evolve	VBP
cord-263987-ff6kor0c	40	71	into	into	IN
cord-263987-ff6kor0c	40	72	state	state	NN
cord-263987-ff6kor0c	40	73	k	k	NN
cord-263987-ff6kor0c	40	74	,	,	,
cord-263987-ff6kor0c	40	75	then	then	RB
cord-263987-ff6kor0c	40	76	summing	sum	VBG
cord-263987-ff6kor0c	40	77	out	out	RP
cord-263987-ff6kor0c	40	78	j	j	NNP
cord-263987-ff6kor0c	40	79	has	have	VBZ
cord-263987-ff6kor0c	40	80	the	the	DT
cord-263987-ff6kor0c	40	81	expected	expect	VBN
cord-263987-ff6kor0c	40	82	result	result	NN
cord-263987-ff6kor0c	40	83	:	:	:
cord-263987-ff6kor0c	40	84	This	this	DT
cord-263987-ff6kor0c	40	85	is	be	VBZ
cord-263987-ff6kor0c	40	86	one	one	CD
cord-263987-ff6kor0c	40	87	way	way	NN
cord-263987-ff6kor0c	40	88	of	of	IN
cord-263987-ff6kor0c	40	89	stating	state	VBG
cord-263987-ff6kor0c	40	90	the	the	DT
cord-263987-ff6kor0c	40	91	defining	define	VBG
cord-263987-ff6kor0c	40	92	property	property	NN
cord-263987-ff6kor0c	40	93	of	of	IN
cord-263987-ff6kor0c	40	94	a	a	DT
cord-263987-ff6kor0c	40	95	Markov	Markov	NNP
cord-263987-ff6kor0c	40	96	chain	chain	NN
cord-263987-ff6kor0c	40	97	:	:	:
cord-263987-ff6kor0c	40	98	its	-PRON-	PRP$
cord-263987-ff6kor0c	40	99	lack	lack	NN
cord-263987-ff6kor0c	40	100	of	of	IN
cord-263987-ff6kor0c	40	101	historical	historical	JJ
cord-263987-ff6kor0c	40	102	memory	memory	NN
cord-263987-ff6kor0c	40	103	previous	previous	JJ
cord-263987-ff6kor0c	40	104	to	to	IN
cord-263987-ff6kor0c	40	105	its	-PRON-	PRP$
cord-263987-ff6kor0c	40	106	current	current	JJ
cord-263987-ff6kor0c	40	107	state	state	NN
cord-263987-ff6kor0c	40	108	.	.	.
cord-263987-ff6kor0c	41	1	Equation	equation	NN
cord-263987-ff6kor0c	41	2	1	1	CD
cord-263987-ff6kor0c	41	3	is	be	VBZ
cord-263987-ff6kor0c	41	4	just	just	RB
cord-263987-ff6kor0c	41	5	an	an	DT
cord-263987-ff6kor0c	41	6	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	41	7	version	version	NN
cord-263987-ff6kor0c	41	8	of	of	IN
cord-263987-ff6kor0c	41	9	this	this	DT
cord-263987-ff6kor0c	41	10	equation	equation	NN
cord-263987-ff6kor0c	41	11	,	,	,
cord-263987-ff6kor0c	41	12	and	and	CC
cord-263987-ff6kor0c	41	13	Eq	Eq	NNP
cord-263987-ff6kor0c	41	14	.	.	.
cord-263987-ff6kor0c	42	1	3	3	CD
cord-263987-ff6kor0c	42	2	is	be	VBZ
cord-263987-ff6kor0c	42	3	the	the	DT
cord-263987-ff6kor0c	42	4	same	same	JJ
cord-263987-ff6kor0c	42	5	equation	equation	NN
cord-263987-ff6kor0c	42	6	in	in	IN
cord-263987-ff6kor0c	42	7	matrix	matrix	NN
cord-263987-ff6kor0c	42	8	form	form	NN
cord-263987-ff6kor0c	42	9	.	.	.
cord-263987-ff6kor0c	43	1	The	the	DT
cord-263987-ff6kor0c	43	2	conditional	conditional	JJ
cord-263987-ff6kor0c	43	3	likelihood	likelihood	NN
cord-263987-ff6kor0c	43	4	for	for	IN
cord-263987-ff6kor0c	43	5	an	an	DT
cord-263987-ff6kor0c	43	6	ancestor	ancestor	NN
cord-263987-ff6kor0c	43	7	-	-	HYPH
cord-263987-ff6kor0c	43	8	descendant	descendant	JJ
cord-263987-ff6kor0c	43	9	pair	pair	NN
cord-263987-ff6kor0c	43	10	can	can	MD
cord-263987-ff6kor0c	43	11	be	be	VB
cord-263987-ff6kor0c	43	12	converted	convert	VBN
cord-263987-ff6kor0c	43	13	into	into	IN
cord-263987-ff6kor0c	43	14	a	a	DT
cord-263987-ff6kor0c	43	15	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	43	16	likelihood	likelihood	NN
cord-263987-ff6kor0c	43	17	for	for	IN
cord-263987-ff6kor0c	43	18	a	a	DT
cord-263987-ff6kor0c	43	19	set	set	NN
cord-263987-ff6kor0c	43	20	of	of	IN
cord-263987-ff6kor0c	43	21	extant	extant	JJ
cord-263987-ff6kor0c	43	22	taxon	taxon	NN
cord-263987-ff6kor0c	43	23	states	state	NNS
cord-263987-ff6kor0c	43	24	S	S	NNS
cord-263987-ff6kor0c	43	25	related	relate	VBN
cord-263987-ff6kor0c	43	26	by	by	IN
cord-263987-ff6kor0c	43	27	a	a	DT
cord-263987-ff6kor0c	43	28	tree	tree	NN
cord-263987-ff6kor0c	43	29	T	T	NNP
cord-263987-ff6kor0c	43	30	,	,	,
cord-263987-ff6kor0c	43	31	as	as	IN
cord-263987-ff6kor0c	43	32	follows	follow	VBZ
cord-263987-ff6kor0c	43	33	.	.	.
cord-263987-ff6kor0c	44	1	(	(	-LRB-
cord-263987-ff6kor0c	44	2	I	-PRON-	PRP
cord-263987-ff6kor0c	44	3	assume	assume	VBP
cord-263987-ff6kor0c	44	4	for	for	IN
cord-263987-ff6kor0c	44	5	convenience	convenience	NN
cord-263987-ff6kor0c	44	6	that	that	WDT
cord-263987-ff6kor0c	44	7	T	T	NNP
cord-263987-ff6kor0c	44	8	is	be	VBZ
cord-263987-ff6kor0c	44	9	a	a	DT
cord-263987-ff6kor0c	44	10	binary	binary	JJ
cord-263987-ff6kor0c	44	11	tree	tree	NN
cord-263987-ff6kor0c	44	12	,	,	,
cord-263987-ff6kor0c	44	13	though	though	IN
cord-263987-ff6kor0c	44	14	relaxing	relax	VBG
cord-263987-ff6kor0c	44	15	this	this	DT
cord-263987-ff6kor0c	44	16	constraint	constraint	NN
cord-263987-ff6kor0c	44	17	is	be	VBZ
cord-263987-ff6kor0c	44	18	straightforward	straightforward	JJ
cord-263987-ff6kor0c	44	19	.	.	.
cord-263987-ff6kor0c	44	20	)	)	-RRB-
cord-263987-ff6kor0c	45	1	To	to	TO
cord-263987-ff6kor0c	45	2	compute	compute	VB
cord-263987-ff6kor0c	45	3	the	the	DT
cord-263987-ff6kor0c	45	4	likelihood	likelihood	NN
cord-263987-ff6kor0c	45	5	requires	require	VBZ
cord-263987-ff6kor0c	45	6	that	that	IN
cord-263987-ff6kor0c	45	7	one	one	CD
cord-263987-ff6kor0c	45	8	first	first	NN
cord-263987-ff6kor0c	45	9	computes	compute	VBZ
cord-263987-ff6kor0c	45	10	,	,	,
cord-263987-ff6kor0c	45	11	for	for	IN
cord-263987-ff6kor0c	45	12	every	every	DT
cord-263987-ff6kor0c	45	13	node	node	NN
cord-263987-ff6kor0c	45	14	n	n	CC
cord-263987-ff6kor0c	45	15	in	in	IN
cord-263987-ff6kor0c	45	16	the	the	DT
cord-263987-ff6kor0c	45	17	tree	tree	NN
cord-263987-ff6kor0c	45	18	,	,	,
cord-263987-ff6kor0c	45	19	the	the	DT
cord-263987-ff6kor0c	45	20	probability	probability	NN
cord-263987-ff6kor0c	45	21	F	F	NNP
cord-263987-ff6kor0c	45	22	i	i	NNP
cord-263987-ff6kor0c	45	23	(	(	-LRB-
cord-263987-ff6kor0c	45	24	n	n	NN
cord-263987-ff6kor0c	45	25	)	)	-RRB-
cord-263987-ff6kor0c	45	26	of	of	IN
cord-263987-ff6kor0c	45	27	all	all	DT
cord-263987-ff6kor0c	45	28	observed	observe	VBN
cord-263987-ff6kor0c	45	29	states	state	NNS
cord-263987-ff6kor0c	45	30	at	at	IN
cord-263987-ff6kor0c	45	31	leaf	leaf	NN
cord-263987-ff6kor0c	45	32	nodes	node	NNS
cord-263987-ff6kor0c	45	33	descended	descend	VBD
cord-263987-ff6kor0c	45	34	from	from	IN
cord-263987-ff6kor0c	45	35	node	node	NNP
cord-263987-ff6kor0c	45	36	n	n	NNP
cord-263987-ff6kor0c	45	37	,	,	,
cord-263987-ff6kor0c	45	38	conditioned	condition	VBN
cord-263987-ff6kor0c	45	39	on	on	IN
cord-263987-ff6kor0c	45	40	node	node	NN
cord-263987-ff6kor0c	45	41	n	n	NN
cord-263987-ff6kor0c	45	42	being	be	VBG
cord-263987-ff6kor0c	45	43	in	in	IN
cord-263987-ff6kor0c	45	44	state	state	NN
cord-263987-ff6kor0c	45	45	i.	i.	NN
cord-263987-ff6kor0c	46	1	This	this	DT
cord-263987-ff6kor0c	46	2	is	be	VBZ
cord-263987-ff6kor0c	46	3	given	give	VBN
cord-263987-ff6kor0c	46	4	by	by	IN
cord-263987-ff6kor0c	46	5	Felsenstein	Felsenstein	NNP
cord-263987-ff6kor0c	46	6	's	's	POS
cord-263987-ff6kor0c	46	7	pruning	pruning	NN
cord-263987-ff6kor0c	46	8	recursion	recursion	NN
cord-263987-ff6kor0c	46	9	:	:	:
cord-263987-ff6kor0c	46	10	if	if	IN
cord-263987-ff6kor0c	46	11	n	n	NN
cord-263987-ff6kor0c	46	12	is	be	VBZ
cord-263987-ff6kor0c	46	13	a	a	DT
cord-263987-ff6kor0c	46	14	leaf	leaf	NN
cord-263987-ff6kor0c	46	15	node	node	NN
cord-263987-ff6kor0c	46	16	in	in	IN
cord-263987-ff6kor0c	46	17	state	state	NN
cord-263987-ff6kor0c	46	18	s	s	NNP
cord-263987-ff6kor0c	46	19	n	n	NN
cord-263987-ff6kor0c	46	20	(	(	-LRB-
cord-263987-ff6kor0c	46	21	4	4	CD
cord-263987-ff6kor0c	46	22	)	)	-RRB-
cord-263987-ff6kor0c	46	23	where	where	WRB
cord-263987-ff6kor0c	46	24	t	t	NNP
cord-263987-ff6kor0c	46	25	mn	mn	NNP
cord-263987-ff6kor0c	46	26	denotes	denote	VBZ
cord-263987-ff6kor0c	46	27	the	the	DT
cord-263987-ff6kor0c	46	28	length	length	NN
cord-263987-ff6kor0c	46	29	of	of	IN
cord-263987-ff6kor0c	46	30	the	the	DT
cord-263987-ff6kor0c	46	31	branch	branch	NN
cord-263987-ff6kor0c	46	32	from	from	IN
cord-263987-ff6kor0c	46	33	tree	tree	NN
cord-263987-ff6kor0c	46	34	node	node	NN
cord-263987-ff6kor0c	46	35	m	m	NN
cord-263987-ff6kor0c	46	36	to	to	IN
cord-263987-ff6kor0c	46	37	tree	tree	NN
cord-263987-ff6kor0c	46	38	node	node	NN
cord-263987-ff6kor0c	46	39	n.	n.	NN
cord-263987-ff6kor0c	47	1	I	-PRON-	PRP
cord-263987-ff6kor0c	47	2	have	have	VBP
cord-263987-ff6kor0c	47	3	used	use	VBN
cord-263987-ff6kor0c	47	4	the	the	DT
cord-263987-ff6kor0c	47	5	notation	notation	NN
cord-263987-ff6kor0c	47	6	(	(	-LRB-
cord-263987-ff6kor0c	47	7	j	j	NNP
cord-263987-ff6kor0c	47	8	)	)	-RRB-
cord-263987-ff6kor0c	47	9	for	for	IN
cord-263987-ff6kor0c	47	10	the	the	DT
cord-263987-ff6kor0c	47	11	unit	unit	NN
cord-263987-ff6kor0c	47	12	vector	vector	NN
cord-263987-ff6kor0c	47	13	in	in	IN
cord-263987-ff6kor0c	47	14	dimension	dimension	NN
cord-263987-ff6kor0c	47	15	j	j	NNP
cord-263987-ff6kor0c	47	16	,	,	,
cord-263987-ff6kor0c	47	17	and	and	CC
cord-263987-ff6kor0c	47	18	the	the	DT
cord-263987-ff6kor0c	47	19	symbol	symbol	NN
cord-263987-ff6kor0c	47	20	•	•	NNP
cord-263987-ff6kor0c	47	21	to	to	TO
cord-263987-ff6kor0c	47	22	denote	denote	VB
cord-263987-ff6kor0c	48	1	the	the	DT
cord-263987-ff6kor0c	48	2	Hadamard	Hadamard	NNP
cord-263987-ff6kor0c	48	3	product	product	NN
cord-263987-ff6kor0c	48	4	(	(	-LRB-
cord-263987-ff6kor0c	48	5	also	also	RB
cord-263987-ff6kor0c	48	6	known	know	VBN
cord-263987-ff6kor0c	48	7	as	as	IN
cord-263987-ff6kor0c	48	8	the	the	DT
cord-263987-ff6kor0c	48	9	pointwise	pointwise	JJ
cord-263987-ff6kor0c	48	10	product	product	NN
cord-263987-ff6kor0c	48	11	)	)	-RRB-
cord-263987-ff6kor0c	48	12	,	,	,
cord-263987-ff6kor0c	48	13	defined	define	VBN
cord-263987-ff6kor0c	48	14	such	such	JJ
cord-263987-ff6kor0c	48	15	that	that	IN
cord-263987-ff6kor0c	48	16	for	for	IN
cord-263987-ff6kor0c	48	17	any	any	DT
cord-263987-ff6kor0c	48	18	two	two	CD
cord-263987-ff6kor0c	48	19	vectors	vector	NNS
cord-263987-ff6kor0c	48	20	u	u	NN
cord-263987-ff6kor0c	48	21	,	,	,
cord-263987-ff6kor0c	48	22	v	v	NN
cord-263987-ff6kor0c	48	23	of	of	IN
cord-263987-ff6kor0c	48	24	the	the	DT
cord-263987-ff6kor0c	48	25	same	same	JJ
cord-263987-ff6kor0c	48	26	size	size	NN
cord-263987-ff6kor0c	48	27	:	:	:
cord-263987-ff6kor0c	48	28	Supposing	suppose	VBG
cord-263987-ff6kor0c	48	29	that	that	DT
cord-263987-ff6kor0c	48	30	node	node	NN
cord-263987-ff6kor0c	48	31	1	1	CD
cord-263987-ff6kor0c	48	32	is	be	VBZ
cord-263987-ff6kor0c	48	33	the	the	DT
cord-263987-ff6kor0c	48	34	root	root	NN
cord-263987-ff6kor0c	48	35	node	node	NN
cord-263987-ff6kor0c	48	36	of	of	IN
cord-263987-ff6kor0c	48	37	the	the	DT
cord-263987-ff6kor0c	48	38	tree	tree	NN
cord-263987-ff6kor0c	48	39	,	,	,
cord-263987-ff6kor0c	48	40	and	and	CC
cord-263987-ff6kor0c	48	41	that	that	IN
cord-263987-ff6kor0c	48	42	the	the	DT
cord-263987-ff6kor0c	48	43	distribution	distribution	NN
cord-263987-ff6kor0c	48	44	of	of	IN
cord-263987-ff6kor0c	48	45	states	state	NNS
cord-263987-ff6kor0c	48	46	at	at	IN
cord-263987-ff6kor0c	48	47	this	this	DT
cord-263987-ff6kor0c	48	48	root	root	NN
cord-263987-ff6kor0c	48	49	node	node	NN
cord-263987-ff6kor0c	48	50	is	be	VBZ
cord-263987-ff6kor0c	48	51	given	give	VBN
cord-263987-ff6kor0c	48	52	by	by	IN
cord-263987-ff6kor0c	48	53	ρ	ρ	NNP
cord-263987-ff6kor0c	48	54	,	,	,
cord-263987-ff6kor0c	48	55	the	the	DT
cord-263987-ff6kor0c	48	56	likelihood	likelihood	NN
cord-263987-ff6kor0c	48	57	can	can	MD
cord-263987-ff6kor0c	48	58	be	be	VB
cord-263987-ff6kor0c	48	59	written	write	VBN
cord-263987-ff6kor0c	48	60	as	as	IN
cord-263987-ff6kor0c	48	61	where	where	WRB
cord-263987-ff6kor0c	48	62	u	u	NNP
cord-263987-ff6kor0c	48	63	·	·	NFP
cord-263987-ff6kor0c	48	64	v	v	NNP
cord-263987-ff6kor0c	48	65	denotes	denote	VBZ
cord-263987-ff6kor0c	48	66	the	the	DT
cord-263987-ff6kor0c	48	67	scalar	scalar	JJ
cord-263987-ff6kor0c	48	68	product	product	NN
cord-263987-ff6kor0c	48	69	of	of	IN
cord-263987-ff6kor0c	48	70	u	u	NNP
cord-263987-ff6kor0c	48	71	and	and	CC
cord-263987-ff6kor0c	48	72	v.	v.	NNP
cord-263987-ff6kor0c	49	1	It	-PRON-	PRP
cord-263987-ff6kor0c	49	2	is	be	VBZ
cord-263987-ff6kor0c	49	3	common	common	JJ
cord-263987-ff6kor0c	49	4	to	to	TO
cord-263987-ff6kor0c	49	5	assume	assume	VB
cord-263987-ff6kor0c	49	6	that	that	IN
cord-263987-ff6kor0c	49	7	the	the	DT
cord-263987-ff6kor0c	49	8	root	root	NN
cord-263987-ff6kor0c	49	9	node	node	NN
cord-263987-ff6kor0c	49	10	is	be	VBZ
cord-263987-ff6kor0c	49	11	at	at	IN
cord-263987-ff6kor0c	49	12	equilibrium	equilibrium	NN
cord-263987-ff6kor0c	49	13	,	,	,
cord-263987-ff6kor0c	49	14	so	so	IN
cord-263987-ff6kor0c	49	15	that	that	IN
cord-263987-ff6kor0c	49	16	ρ	ρ	NN
cord-263987-ff6kor0c	49	17	=	=	SYM
cord-263987-ff6kor0c	49	18	π	π	NN
cord-263987-ff6kor0c	49	19	.	.	.
cord-263987-ff6kor0c	50	1	As	as	IN
cord-263987-ff6kor0c	50	2	mentioned	mention	VBN
cord-263987-ff6kor0c	50	3	above	above	RB
cord-263987-ff6kor0c	50	4	,	,	,
cord-263987-ff6kor0c	50	5	this	this	DT
cord-263987-ff6kor0c	50	6	mathematical	mathematical	JJ
cord-263987-ff6kor0c	50	7	approach	approach	NN
cord-263987-ff6kor0c	50	8	is	be	VBZ
cord-263987-ff6kor0c	50	9	fundamental	fundamental	JJ
cord-263987-ff6kor0c	50	10	to	to	IN
cord-263987-ff6kor0c	50	11	statistical	statistical	JJ
cord-263987-ff6kor0c	50	12	phylogenetics	phylogenetic	NNS
cord-263987-ff6kor0c	50	13	and	and	CC
cord-263987-ff6kor0c	50	14	many	many	JJ
cord-263987-ff6kor0c	50	15	applications	application	NNS
cord-263987-ff6kor0c	50	16	in	in	IN
cord-263987-ff6kor0c	50	17	bioinformatics	bioinformatic	NNS
cord-263987-ff6kor0c	50	18	.	.	.
cord-263987-ff6kor0c	51	1	For	for	IN
cord-263987-ff6kor0c	51	2	small	small	JJ
cord-263987-ff6kor0c	51	3	state	state	NN
cord-263987-ff6kor0c	51	4	spaces	space	NNS
cord-263987-ff6kor0c	51	5	,	,	,
cord-263987-ff6kor0c	51	6	such	such	JJ
cord-263987-ff6kor0c	51	7	as	as	IN
cord-263987-ff6kor0c	51	8	(	(	-LRB-
cord-263987-ff6kor0c	51	9	for	for	IN
cord-263987-ff6kor0c	51	10	example	example	NN
cord-263987-ff6kor0c	51	11	)	)	-RRB-
cord-263987-ff6kor0c	51	12	the	the	DT
cord-263987-ff6kor0c	51	13	20	20	CD
cord-263987-ff6kor0c	51	14	amino	amino	NN
cord-263987-ff6kor0c	51	15	acids	acid	NNS
cord-263987-ff6kor0c	51	16	or	or	CC
cord-263987-ff6kor0c	51	17	61	61	CD
cord-263987-ff6kor0c	51	18	sense	sense	NN
cord-263987-ff6kor0c	51	19	codons	codon	NNS
cord-263987-ff6kor0c	51	20	,	,	,
cord-263987-ff6kor0c	51	21	the	the	DT
cord-263987-ff6kor0c	51	22	matrix	matrix	NN
cord-263987-ff6kor0c	51	23	exponential	exponential	JJ
cord-263987-ff6kor0c	51	24	M(t	M(t	NNP
cord-263987-ff6kor0c	51	25	)	)	-RRB-
cord-263987-ff6kor0c	51	26	in	in	IN
cord-263987-ff6kor0c	51	27	Eq	Eq	NNP
cord-263987-ff6kor0c	51	28	.	.	.
cord-263987-ff6kor0c	52	1	2	2	LS
cord-263987-ff6kor0c	52	2	can	can	MD
cord-263987-ff6kor0c	52	3	be	be	VB
cord-263987-ff6kor0c	52	4	solved	solve	VBN
cord-263987-ff6kor0c	52	5	exactly	exactly	RB
cord-263987-ff6kor0c	52	6	and	and	CC
cord-263987-ff6kor0c	52	7	practically	practically	RB
cord-263987-ff6kor0c	52	8	by	by	IN
cord-263987-ff6kor0c	52	9	the	the	DT
cord-263987-ff6kor0c	52	10	technique	technique	NN
cord-263987-ff6kor0c	52	11	of	of	IN
cord-263987-ff6kor0c	52	12	spectral	spectral	JJ
cord-263987-ff6kor0c	52	13	decomposition	decomposition	NN
cord-263987-ff6kor0c	52	14	(	(	-LRB-
cord-263987-ff6kor0c	52	15	i.e.	i.e.	FW
cord-263987-ff6kor0c	52	16	finding	find	VBG
cord-263987-ff6kor0c	52	17	eigenvalues	eigenvalue	NNS
cord-263987-ff6kor0c	52	18	and	and	CC
cord-263987-ff6kor0c	52	19	eigenvectors	eigenvector	NNS
cord-263987-ff6kor0c	52	20	)	)	-RRB-
cord-263987-ff6kor0c	52	21	.	.	.
cord-263987-ff6kor0c	53	1	Such	such	JJ
cord-263987-ff6kor0c	53	2	an	an	DT
cord-263987-ff6kor0c	53	3	approach	approach	NN
cord-263987-ff6kor0c	53	4	informs	inform	VBZ
cord-263987-ff6kor0c	53	5	the	the	DT
cord-263987-ff6kor0c	53	6	Dayhoff	Dayhoff	NNP
cord-263987-ff6kor0c	53	7	PAM	PAM	NNP
cord-263987-ff6kor0c	53	8	matrix	matrix	NN
cord-263987-ff6kor0c	53	9	.	.	.
cord-263987-ff6kor0c	54	1	It	-PRON-	PRP
cord-263987-ff6kor0c	54	2	was	be	VBD
cord-263987-ff6kor0c	54	3	also	also	RB
cord-263987-ff6kor0c	54	4	solved	solve	VBN
cord-263987-ff6kor0c	54	5	for	for	IN
cord-263987-ff6kor0c	54	6	certain	certain	JJ
cord-263987-ff6kor0c	54	7	specific	specific	JJ
cord-263987-ff6kor0c	54	8	parametric	parametric	JJ
cord-263987-ff6kor0c	54	9	forms	form	NNS
cord-263987-ff6kor0c	54	10	of	of	IN
cord-263987-ff6kor0c	54	11	the	the	DT
cord-263987-ff6kor0c	54	12	rate	rate	NN
cord-263987-ff6kor0c	54	13	matrix	matrix	NN
cord-263987-ff6kor0c	54	14	R	r	NN
cord-263987-ff6kor0c	54	15	by	by	IN
cord-263987-ff6kor0c	54	16	Jukes	Jukes	NNP
cord-263987-ff6kor0c	54	17	and	and	CC
cord-263987-ff6kor0c	54	18	Cantor	Cantor	NNP
cord-263987-ff6kor0c	54	19	[	[	-LRB-
cord-263987-ff6kor0c	54	20	1	1	CD
cord-263987-ff6kor0c	54	21	]	]	-RRB-
cord-263987-ff6kor0c	54	22	,	,	,
cord-263987-ff6kor0c	54	23	Kimura	Kimura	NNP
cord-263987-ff6kor0c	54	24	[	[	-LRB-
cord-263987-ff6kor0c	54	25	31	31	CD
cord-263987-ff6kor0c	54	26	]	]	-RRB-
cord-263987-ff6kor0c	54	27	,	,	,
cord-263987-ff6kor0c	54	28	Felsenstein	Felsenstein	NNP
cord-263987-ff6kor0c	54	29	[	[	-LRB-
cord-263987-ff6kor0c	54	30	3	3	CD
cord-263987-ff6kor0c	54	31	]	]	-RRB-
cord-263987-ff6kor0c	54	32	,	,	,
cord-263987-ff6kor0c	54	33	and	and	CC
cord-263987-ff6kor0c	54	34	Hasegawa	Hasegawa	NNP
cord-263987-ff6kor0c	54	35	et	et	NNP
cord-263987-ff6kor0c	54	36	al	al	NNP
cord-263987-ff6kor0c	54	37	.	.	.
cord-263987-ff6kor0c	55	1	[	[	-LRB-
cord-263987-ff6kor0c	55	2	32	32	CD
cord-263987-ff6kor0c	55	3	]	]	-RRB-
cord-263987-ff6kor0c	55	4	,	,	,
cord-263987-ff6kor0c	55	5	among	among	IN
cord-263987-ff6kor0c	55	6	others	other	NNS
cord-263987-ff6kor0c	55	7	.	.	.
cord-263987-ff6kor0c	56	1	This	this	DT
cord-263987-ff6kor0c	56	2	approach	approach	NN
cord-263987-ff6kor0c	56	3	is	be	VBZ
cord-263987-ff6kor0c	56	4	used	use	VBN
cord-263987-ff6kor0c	56	5	by	by	IN
cord-263987-ff6kor0c	56	6	all	all	DT
cord-263987-ff6kor0c	56	7	likelihood	likelihood	NN
cord-263987-ff6kor0c	56	8	-	-	HYPH
cord-263987-ff6kor0c	56	9	based	base	VBN
cord-263987-ff6kor0c	56	10	phylogenetics	phylogenetic	NNS
cord-263987-ff6kor0c	56	11	tools	tool	NNS
cord-263987-ff6kor0c	56	12	,	,	,
cord-263987-ff6kor0c	56	13	such	such	JJ
cord-263987-ff6kor0c	56	14	as	as	IN
cord-263987-ff6kor0c	56	15	RevBayes	RevBayes	NNPS
cord-263987-ff6kor0c	56	16	[	[	-LRB-
cord-263987-ff6kor0c	56	17	33	33	CD
cord-263987-ff6kor0c	56	18	]	]	-RRB-
cord-263987-ff6kor0c	56	19	,	,	,
cord-263987-ff6kor0c	56	20	BEAST	BEAST	NNP
cord-263987-ff6kor0c	56	21	[	[	-LRB-
cord-263987-ff6kor0c	56	22	34	34	CD
cord-263987-ff6kor0c	56	23	]	]	-RRB-
cord-263987-ff6kor0c	56	24	,	,	,
cord-263987-ff6kor0c	56	25	RAxML	RAxML	VBZ
cord-263987-ff6kor0c	56	26	[	[	-LRB-
cord-263987-ff6kor0c	56	27	35	35	CD
cord-263987-ff6kor0c	56	28	]	]	-RRB-
cord-263987-ff6kor0c	56	29	,	,	,
cord-263987-ff6kor0c	56	30	HyPhy	HyPhy	NNP
cord-263987-ff6kor0c	56	31	[	[	-LRB-
cord-263987-ff6kor0c	56	32	36	36	CD
cord-263987-ff6kor0c	56	33	]	]	-RRB-
cord-263987-ff6kor0c	56	34	,	,	,
cord-263987-ff6kor0c	56	35	PAML	PAML	NNP
cord-263987-ff6kor0c	56	36	[	[	-LRB-
cord-263987-ff6kor0c	56	37	37	37	CD
cord-263987-ff6kor0c	56	38	]	]	-RRB-
cord-263987-ff6kor0c	56	39	,	,	,
cord-263987-ff6kor0c	56	40	PHYLIP	PHYLIP	NNP
cord-263987-ff6kor0c	56	41	[	[	-LRB-
cord-263987-ff6kor0c	56	42	38	38	CD
cord-263987-ff6kor0c	56	43	]	]	-RRB-
cord-263987-ff6kor0c	56	44	,	,	,
cord-263987-ff6kor0c	56	45	TREE	tree	NN
cord-263987-ff6kor0c	56	46	-	-	HYPH
cord-263987-ff6kor0c	56	47	PUZZLE	puzzle	NN
cord-263987-ff6kor0c	56	48	[	[	-LRB-
cord-263987-ff6kor0c	56	49	39	39	CD
cord-263987-ff6kor0c	56	50	]	]	-RRB-
cord-263987-ff6kor0c	56	51	,	,	,
cord-263987-ff6kor0c	56	52	and	and	CC
cord-263987-ff6kor0c	56	53	XRate	XRate	NNP
cord-263987-ff6kor0c	56	54	[	[	-LRB-
cord-263987-ff6kor0c	56	55	40	40	CD
cord-263987-ff6kor0c	56	56	]	]	-RRB-
cord-263987-ff6kor0c	56	57	.	.	.
cord-263987-ff6kor0c	57	1	Many	many	JJ
cord-263987-ff6kor0c	57	2	more	more	JJR
cord-263987-ff6kor0c	57	3	bioinformatics	bioinformatics	NN
cord-263987-ff6kor0c	57	4	tools	tool	NNS
cord-263987-ff6kor0c	57	5	use	use	VBP
cord-263987-ff6kor0c	57	6	the	the	DT
cord-263987-ff6kor0c	57	7	Dayhoff	Dayhoff	NNP
cord-263987-ff6kor0c	57	8	PAM	PAM	NNP
cord-263987-ff6kor0c	57	9	matrix	matrix	NN
cord-263987-ff6kor0c	57	10	or	or	CC
cord-263987-ff6kor0c	57	11	other	other	JJ
cord-263987-ff6kor0c	57	12	substitution	substitution	NN
cord-263987-ff6kor0c	57	13	matrix	matrix	NN
cord-263987-ff6kor0c	57	14	based	base	VBN
cord-263987-ff6kor0c	57	15	on	on	IN
cord-263987-ff6kor0c	57	16	an	an	DT
cord-263987-ff6kor0c	57	17	underlying	underlie	VBG
cord-263987-ff6kor0c	57	18	master	master	NN
cord-263987-ff6kor0c	57	19	equation	equation	NN
cord-263987-ff6kor0c	57	20	of	of	IN
cord-263987-ff6kor0c	57	21	the	the	DT
cord-263987-ff6kor0c	57	22	form	form	NN
cord-263987-ff6kor0c	57	23	Eq	Eq	NNP
cord-263987-ff6kor0c	57	24	.	.	.
cord-263987-ff6kor0c	58	1	1	1	LS
cord-263987-ff6kor0c	58	2	.	.	.
cord-263987-ff6kor0c	59	1	There	there	EX
cord-263987-ff6kor0c	59	2	exists	exist	VBZ
cord-263987-ff6kor0c	59	3	a	a	DT
cord-263987-ff6kor0c	59	4	deep	deep	JJ
cord-263987-ff6kor0c	59	5	literature	literature	NN
cord-263987-ff6kor0c	59	6	on	on	IN
cord-263987-ff6kor0c	59	7	Markov	Markov	NNP
cord-263987-ff6kor0c	59	8	chains	chain	NNS
cord-263987-ff6kor0c	59	9	,	,	,
cord-263987-ff6kor0c	59	10	to	to	TO
cord-263987-ff6kor0c	59	11	which	which	WDT
cord-263987-ff6kor0c	59	12	this	this	DT
cord-263987-ff6kor0c	59	13	brief	brief	JJ
cord-263987-ff6kor0c	59	14	survey	survey	NN
cord-263987-ff6kor0c	59	15	can	can	MD
cord-263987-ff6kor0c	59	16	not	not	RB
cord-263987-ff6kor0c	59	17	remotely	remotely	RB
cord-263987-ff6kor0c	59	18	do	do	VB
cord-263987-ff6kor0c	59	19	justice	justice	NN
cord-263987-ff6kor0c	59	20	,	,	,
cord-263987-ff6kor0c	59	21	but	but	CC
cord-263987-ff6kor0c	59	22	several	several	JJ
cord-263987-ff6kor0c	59	23	concepts	concept	NNS
cord-263987-ff6kor0c	59	24	must	must	MD
cord-263987-ff6kor0c	59	25	be	be	VB
cord-263987-ff6kor0c	59	26	mentioned	mention	VBN
cord-263987-ff6kor0c	59	27	in	in	IN
cord-263987-ff6kor0c	59	28	order	order	NN
cord-263987-ff6kor0c	59	29	to	to	TO
cord-263987-ff6kor0c	59	30	survey	survey	VB
cord-263987-ff6kor0c	59	31	progress	progress	NN
cord-263987-ff6kor0c	59	32	in	in	IN
cord-263987-ff6kor0c	59	33	this	this	DT
cord-263987-ff6kor0c	59	34	area	area	NN
cord-263987-ff6kor0c	59	35	.	.	.
cord-263987-ff6kor0c	60	1	A	a	DT
cord-263987-ff6kor0c	60	2	Markov	Markov	NNP
cord-263987-ff6kor0c	60	3	chain	chain	NN
cord-263987-ff6kor0c	60	4	is	be	VBZ
cord-263987-ff6kor0c	60	5	time	time	NN
cord-263987-ff6kor0c	60	6	-	-	HYPH
cord-263987-ff6kor0c	60	7	homogeneous	homogeneous	JJ
cord-263987-ff6kor0c	60	8	if	if	IN
cord-263987-ff6kor0c	60	9	the	the	DT
cord-263987-ff6kor0c	60	10	elements	element	NNS
cord-263987-ff6kor0c	60	11	of	of	IN
cord-263987-ff6kor0c	60	12	the	the	DT
cord-263987-ff6kor0c	60	13	rate	rate	NN
cord-263987-ff6kor0c	60	14	matrix	matrix	NN
cord-263987-ff6kor0c	60	15	R	r	NN
cord-263987-ff6kor0c	60	16	in	in	IN
cord-263987-ff6kor0c	60	17	Eq	Eq	NNP
cord-263987-ff6kor0c	60	18	.	.	.
cord-263987-ff6kor0c	61	1	1	1	CD
cord-263987-ff6kor0c	61	2	are	be	VBP
cord-263987-ff6kor0c	61	3	themselves	-PRON-	PRP
cord-263987-ff6kor0c	61	4	independent	independent	JJ
cord-263987-ff6kor0c	61	5	of	of	IN
cord-263987-ff6kor0c	61	6	time	time	NN
cord-263987-ff6kor0c	61	7	.	.	.
cord-263987-ff6kor0c	62	1	If	if	IN
cord-263987-ff6kor0c	62	2	a	a	DT
cord-263987-ff6kor0c	62	3	Markov	Markov	NNP
cord-263987-ff6kor0c	62	4	chain	chain	NN
cord-263987-ff6kor0c	62	5	is	be	VBZ
cord-263987-ff6kor0c	62	6	time	time	NN
cord-263987-ff6kor0c	62	7	-	-	HYPH
cord-263987-ff6kor0c	62	8	homogeneous	homogeneous	JJ
cord-263987-ff6kor0c	62	9	and	and	CC
cord-263987-ff6kor0c	62	10	is	be	VBZ
cord-263987-ff6kor0c	62	11	known	know	VBN
cord-263987-ff6kor0c	62	12	to	to	TO
cord-263987-ff6kor0c	62	13	be	be	VB
cord-263987-ff6kor0c	62	14	in	in	IN
cord-263987-ff6kor0c	62	15	equilibrium	equilibrium	NN
cord-263987-ff6kor0c	62	16	at	at	IN
cord-263987-ff6kor0c	62	17	a	a	DT
cord-263987-ff6kor0c	62	18	given	give	VBN
cord-263987-ff6kor0c	62	19	time	time	NN
cord-263987-ff6kor0c	62	20	,	,	,
cord-263987-ff6kor0c	62	21	for	for	IN
cord-263987-ff6kor0c	62	22	example	example	NN
cord-263987-ff6kor0c	62	23	p(0	p(0	NNP
cord-263987-ff6kor0c	62	24	)	)	-RRB-
cord-263987-ff6kor0c	62	25	=	=	NFP
cord-263987-ff6kor0c	63	1	π	π	LS
cord-263987-ff6kor0c	64	1	,	,	,
cord-263987-ff6kor0c	64	2	then	then	RB
cord-263987-ff6kor0c	64	3	(	(	-LRB-
cord-263987-ff6kor0c	64	4	absent	absent	VB
cord-263987-ff6kor0c	64	5	any	any	DT
cord-263987-ff6kor0c	64	6	other	other	JJ
cord-263987-ff6kor0c	64	7	constraints	constraint	NNS
cord-263987-ff6kor0c	64	8	)	)	-RRB-
cord-263987-ff6kor0c	64	9	it	-PRON-	PRP
cord-263987-ff6kor0c	64	10	will	will	MD
cord-263987-ff6kor0c	64	11	be	be	VB
cord-263987-ff6kor0c	64	12	in	in	IN
cord-263987-ff6kor0c	64	13	equilibrium	equilibrium	NN
cord-263987-ff6kor0c	64	14	at	at	IN
cord-263987-ff6kor0c	64	15	all	all	DT
cord-263987-ff6kor0c	64	16	times	time	NNS
cord-263987-ff6kor0c	64	17	;	;	:
cord-263987-ff6kor0c	64	18	such	such	PDT
cord-263987-ff6kor0c	64	19	a	a	DT
cord-263987-ff6kor0c	64	20	chain	chain	NN
cord-263987-ff6kor0c	64	21	is	be	VBZ
cord-263987-ff6kor0c	64	22	referred	refer	VBN
cord-263987-ff6kor0c	64	23	to	to	IN
cord-263987-ff6kor0c	64	24	as	as	IN
cord-263987-ff6kor0c	64	25	being	be	VBG
cord-263987-ff6kor0c	64	26	stationary	stationary	JJ
cord-263987-ff6kor0c	64	27	.	.	.
cord-263987-ff6kor0c	65	1	The	the	DT
cord-263987-ff6kor0c	65	2	time	time	NN
cord-263987-ff6kor0c	65	3	-	-	HYPH
cord-263987-ff6kor0c	65	4	scaling	scaling	NN
cord-263987-ff6kor0c	65	5	of	of	IN
cord-263987-ff6kor0c	65	6	these	these	DT
cord-263987-ff6kor0c	65	7	models	model	NNS
cord-263987-ff6kor0c	65	8	is	be	VBZ
cord-263987-ff6kor0c	65	9	somewhat	somewhat	RB
cord-263987-ff6kor0c	65	10	arbitrary	arbitrary	JJ
cord-263987-ff6kor0c	65	11	:	:	:
cord-263987-ff6kor0c	65	12	if	if	IN
cord-263987-ff6kor0c	65	13	the	the	DT
cord-263987-ff6kor0c	65	14	time	time	NN
cord-263987-ff6kor0c	65	15	parameter	parameter	NN
cord-263987-ff6kor0c	65	16	t	t	NNP
cord-263987-ff6kor0c	65	17	is	be	VBZ
cord-263987-ff6kor0c	65	18	replaced	replace	VBN
cord-263987-ff6kor0c	65	19	by	by	IN
cord-263987-ff6kor0c	65	20	a	a	DT
cord-263987-ff6kor0c	65	21	scaled	scale	VBN
cord-263987-ff6kor0c	65	22	version	version	NN
cord-263987-ff6kor0c	65	23	t	t	NN
cord-263987-ff6kor0c	65	24	/	/	SYM
cord-263987-ff6kor0c	65	25	κ	κ	NNP
cord-263987-ff6kor0c	65	26	,	,	,
cord-263987-ff6kor0c	65	27	while	while	IN
cord-263987-ff6kor0c	65	28	the	the	DT
cord-263987-ff6kor0c	65	29	rate	rate	NN
cord-263987-ff6kor0c	65	30	matrix	matrix	NN
cord-263987-ff6kor0c	65	31	R	r	NN
cord-263987-ff6kor0c	65	32	is	be	VBZ
cord-263987-ff6kor0c	65	33	replaced	replace	VBN
cord-263987-ff6kor0c	65	34	by	by	IN
cord-263987-ff6kor0c	65	35	Rκ	Rκ	NNP
cord-263987-ff6kor0c	65	36	,	,	,
cord-263987-ff6kor0c	65	37	then	then	RB
cord-263987-ff6kor0c	65	38	the	the	DT
cord-263987-ff6kor0c	65	39	likelihood	likelihood	NN
cord-263987-ff6kor0c	65	40	in	in	IN
cord-263987-ff6kor0c	65	41	Eq	Eq	NNP
cord-263987-ff6kor0c	65	42	.	.	.
cord-263987-ff6kor0c	66	1	2	2	CD
cord-263987-ff6kor0c	66	2	is	be	VBZ
cord-263987-ff6kor0c	66	3	unchanged	unchanged	JJ
cord-263987-ff6kor0c	66	4	.	.	.
cord-263987-ff6kor0c	67	1	For	for	IN
cord-263987-ff6kor0c	67	2	some	some	DT
cord-263987-ff6kor0c	67	3	models	model	NNS
cord-263987-ff6kor0c	67	4	,	,	,
cord-263987-ff6kor0c	67	5	the	the	DT
cord-263987-ff6kor0c	67	6	rate	rate	NN
cord-263987-ff6kor0c	67	7	is	be	VBZ
cord-263987-ff6kor0c	67	8	allowed	allow	VBN
cord-263987-ff6kor0c	67	9	to	to	TO
cord-263987-ff6kor0c	67	10	vary	vary	VB
cord-263987-ff6kor0c	67	11	between	between	IN
cord-263987-ff6kor0c	67	12	sites	site	NNS
cord-263987-ff6kor0c	67	13	[	[	-LRB-
cord-263987-ff6kor0c	67	14	4	4	CD
cord-263987-ff6kor0c	67	15	,	,	,
cord-263987-ff6kor0c	67	16	5	5	CD
cord-263987-ff6kor0c	67	17	]	]	-RRB-
cord-263987-ff6kor0c	67	18	.	.	.
cord-263987-ff6kor0c	68	1	A	a	DT
cord-263987-ff6kor0c	68	2	Markov	Markov	NNP
cord-263987-ff6kor0c	68	3	chain	chain	NN
cord-263987-ff6kor0c	68	4	is	be	VBZ
cord-263987-ff6kor0c	68	5	reversible	reversible	JJ
cord-263987-ff6kor0c	68	6	if	if	IN
cord-263987-ff6kor0c	68	7	it	-PRON-	PRP
cord-263987-ff6kor0c	68	8	satisfies	satisfy	VBZ
cord-263987-ff6kor0c	68	9	the	the	DT
cord-263987-ff6kor0c	68	10	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	68	11	detailed	detailed	JJ
cord-263987-ff6kor0c	68	12	balance	balance	NN
cord-263987-ff6kor0c	68	13	condition	condition	NN
cord-263987-ff6kor0c	69	1	π	π	LS
cord-263987-ff6kor0c	70	1	i	i	PRP
cord-263987-ff6kor0c	70	2	R	r	VBP
cord-263987-ff6kor0c	70	3	i	i	NN
cord-263987-ff6kor0c	70	4	,	,	,
cord-263987-ff6kor0c	70	5	j	j	NNP
cord-263987-ff6kor0c	70	6	=	=	SYM
cord-263987-ff6kor0c	70	7	π	π	NNP
cord-263987-ff6kor0c	70	8	j	j	NNP
cord-263987-ff6kor0c	70	9	R	R	NNP
cord-263987-ff6kor0c	70	10	j	j	NNP
cord-263987-ff6kor0c	70	11	,	,	,
cord-263987-ff6kor0c	70	12	i	i	PRP
cord-263987-ff6kor0c	70	13	,	,	,
cord-263987-ff6kor0c	70	14	or	or	CC
cord-263987-ff6kor0c	70	15	its	-PRON-	PRP$
cord-263987-ff6kor0c	70	16	finite	finite	JJ
cord-263987-ff6kor0c	70	17	-	-	HYPH
cord-263987-ff6kor0c	70	18	time	time	NN
cord-263987-ff6kor0c	70	19	equivalent	equivalent	JJ
cord-263987-ff6kor0c	71	1	π	π	LS
cord-263987-ff6kor0c	72	1	i	i	PRP
cord-263987-ff6kor0c	73	1	M	M	NNP
cord-263987-ff6kor0c	73	2	i	i	NNP
cord-263987-ff6kor0c	73	3	,	,	,
cord-263987-ff6kor0c	73	4	j	j	NNP
cord-263987-ff6kor0c	73	5	=	=	SYM
cord-263987-ff6kor0c	73	6	π	π	NNP
cord-263987-ff6kor0c	73	7	j	j	NNP
cord-263987-ff6kor0c	73	8	M	M	NNP
cord-263987-ff6kor0c	73	9	j	j	NNP
cord-263987-ff6kor0c	73	10	,	,	,
cord-263987-ff6kor0c	73	11	i	i	PRP
cord-263987-ff6kor0c	73	12	.	.	.
cord-263987-ff6kor0c	74	1	This	this	DT
cord-263987-ff6kor0c	74	2	amounts	amount	VBZ
cord-263987-ff6kor0c	74	3	to	to	IN
cord-263987-ff6kor0c	74	4	a	a	DT
cord-263987-ff6kor0c	74	5	symmetry	symmetry	NN
cord-263987-ff6kor0c	74	6	constraint	constraint	NN
cord-263987-ff6kor0c	74	7	on	on	IN
cord-263987-ff6kor0c	74	8	the	the	DT
cord-263987-ff6kor0c	74	9	parameter	parameter	NN
cord-263987-ff6kor0c	74	10	space	space	NN
cord-263987-ff6kor0c	74	11	of	of	IN
cord-263987-ff6kor0c	74	12	the	the	DT
cord-263987-ff6kor0c	74	13	chain	chain	NN
cord-263987-ff6kor0c	74	14	(	(	-LRB-
cord-263987-ff6kor0c	74	15	specifically	specifically	RB
cord-263987-ff6kor0c	74	16	,	,	,
cord-263987-ff6kor0c	74	17	the	the	DT
cord-263987-ff6kor0c	74	18	matrix	matrix	NN
cord-263987-ff6kor0c	74	19	S	S	NNP
cord-263987-ff6kor0c	74	20	with	with	IN
cord-263987-ff6kor0c	74	21	elements	element	NNS
cord-263987-ff6kor0c	75	1	S	S	NNP
cord-263987-ff6kor0c	75	2	i	i	NNP
cord-263987-ff6kor0c	75	3	,	,	,
cord-263987-ff6kor0c	75	4	j	j	NNP
cord-263987-ff6kor0c	75	5	=	=	NNP
cord-263987-ff6kor0c	76	1	π	π	LS
cord-263987-ff6kor0c	77	1	i	i	PRP
cord-263987-ff6kor0c	77	2	/	/	SYM
cord-263987-ff6kor0c	77	3	π	π	NNP
cord-263987-ff6kor0c	78	1	j	j	NNP
cord-263987-ff6kor0c	78	2	R	R	NNP
cord-263987-ff6kor0c	78	3	i	i	NNP
cord-263987-ff6kor0c	78	4	,	,	,
cord-263987-ff6kor0c	78	5	j	j	NNP
cord-263987-ff6kor0c	78	6	is	be	VBZ
cord-263987-ff6kor0c	78	7	symmetric	symmetric	JJ
cord-263987-ff6kor0c	78	8	)	)	-RRB-
cord-263987-ff6kor0c	78	9	which	which	WDT
cord-263987-ff6kor0c	78	10	has	have	VBZ
cord-263987-ff6kor0c	78	11	several	several	JJ
cord-263987-ff6kor0c	78	12	convenient	convenient	JJ
cord-263987-ff6kor0c	78	13	advantages	advantage	NNS
cord-263987-ff6kor0c	78	14	:	:	:
cord-263987-ff6kor0c	78	15	it	-PRON-	PRP
cord-263987-ff6kor0c	78	16	effectively	effectively	RB
cord-263987-ff6kor0c	78	17	halves	halve	VBZ
cord-263987-ff6kor0c	78	18	the	the	DT
cord-263987-ff6kor0c	78	19	number	number	NN
cord-263987-ff6kor0c	78	20	of	of	IN
cord-263987-ff6kor0c	78	21	parameters	parameter	NNS
cord-263987-ff6kor0c	78	22	that	that	WDT
cord-263987-ff6kor0c	78	23	must	must	MD
cord-263987-ff6kor0c	78	24	be	be	VB
cord-263987-ff6kor0c	78	25	determined	determine	VBN
cord-263987-ff6kor0c	78	26	,	,	,
cord-263987-ff6kor0c	78	27	it	-PRON-	PRP
cord-263987-ff6kor0c	78	28	eases	ease	VBZ
cord-263987-ff6kor0c	78	29	some	some	DT
cord-263987-ff6kor0c	78	30	of	of	IN
cord-263987-ff6kor0c	78	31	the	the	DT
cord-263987-ff6kor0c	78	32	matrix	matrix	NN
cord-263987-ff6kor0c	78	33	manipulations	manipulation	NNS
cord-263987-ff6kor0c	78	34	(	(	-LRB-
cord-263987-ff6kor0c	78	35	symmetric	symmetric	JJ
cord-263987-ff6kor0c	78	36	matrices	matrix	NNS
cord-263987-ff6kor0c	78	37	have	have	VBP
cord-263987-ff6kor0c	78	38	real	real	JJ
cord-263987-ff6kor0c	78	39	eigenvalues	eigenvalue	NNS
cord-263987-ff6kor0c	78	40	and	and	CC
cord-263987-ff6kor0c	78	41	the	the	DT
cord-263987-ff6kor0c	78	42	algorithms	algorithm	NNS
cord-263987-ff6kor0c	78	43	to	to	TO
cord-263987-ff6kor0c	78	44	find	find	VB
cord-263987-ff6kor0c	78	45	them	-PRON-	PRP
cord-263987-ff6kor0c	78	46	are	be	VBP
cord-263987-ff6kor0c	78	47	generally	generally	RB
cord-263987-ff6kor0c	78	48	more	more	RBR
cord-263987-ff6kor0c	78	49	stable	stable	JJ
cord-263987-ff6kor0c	78	50	)	)	-RRB-
cord-263987-ff6kor0c	78	51	,	,	,
cord-263987-ff6kor0c	78	52	and	and	CC
cord-263987-ff6kor0c	78	53	it	-PRON-	PRP
cord-263987-ff6kor0c	78	54	allows	allow	VBZ
cord-263987-ff6kor0c	78	55	for	for	IN
cord-263987-ff6kor0c	78	56	some	some	DT
cord-263987-ff6kor0c	78	57	convenient	convenient	JJ
cord-263987-ff6kor0c	78	58	manipulations	manipulation	NNS
cord-263987-ff6kor0c	78	59	,	,	,
cord-263987-ff6kor0c	78	60	such	such	JJ
cord-263987-ff6kor0c	78	61	as	as	IN
cord-263987-ff6kor0c	78	62	the	the	DT
cord-263987-ff6kor0c	78	63	socalled	socalled	JJ
cord-263987-ff6kor0c	78	64	pulley	pulley	NN
cord-263987-ff6kor0c	78	65	principle	principle	NN
cord-263987-ff6kor0c	78	66	allowing	allow	VBG
cord-263987-ff6kor0c	78	67	for	for	IN
cord-263987-ff6kor0c	78	68	arbitrary	arbitrary	JJ
cord-263987-ff6kor0c	78	69	re	re	NN
cord-263987-ff6kor0c	78	70	-	-	NN
cord-263987-ff6kor0c	78	71	rooting	rooting	NN
cord-263987-ff6kor0c	78	72	of	of	IN
cord-263987-ff6kor0c	78	73	the	the	DT
cord-263987-ff6kor0c	78	74	tree	tree	NN
cord-263987-ff6kor0c	78	75	[	[	-LRB-
cord-263987-ff6kor0c	78	76	3	3	CD
cord-263987-ff6kor0c	78	77	]	]	-RRB-
cord-263987-ff6kor0c	78	78	.	.	.
cord-263987-ff6kor0c	79	1	From	from	IN
cord-263987-ff6kor0c	79	2	another	another	DT
cord-263987-ff6kor0c	79	3	angle	angle	NN
cord-263987-ff6kor0c	79	4	,	,	,
cord-263987-ff6kor0c	79	5	however	however	RB
cord-263987-ff6kor0c	79	6	,	,	,
cord-263987-ff6kor0c	79	7	these	these	DT
cord-263987-ff6kor0c	79	8	supposed	suppose	VBN
cord-263987-ff6kor0c	79	9	advantages	advantage	NNS
cord-263987-ff6kor0c	79	10	may	may	MD
cord-263987-ff6kor0c	79	11	be	be	VB
cord-263987-ff6kor0c	79	12	viewed	view	VBN
cord-263987-ff6kor0c	79	13	as	as	IN
cord-263987-ff6kor0c	79	14	drawbacks	drawback	NNS
cord-263987-ff6kor0c	79	15	:	:	:
cord-263987-ff6kor0c	79	16	reversibility	reversibility	NN
cord-263987-ff6kor0c	79	17	is	be	VBZ
cord-263987-ff6kor0c	79	18	a	a	DT
cord-263987-ff6kor0c	79	19	simplification	simplification	NN
cord-263987-ff6kor0c	79	20	which	which	WDT
cord-263987-ff6kor0c	79	21	ignores	ignore	VBZ
cord-263987-ff6kor0c	79	22	some	some	DT
cord-263987-ff6kor0c	79	23	unreversible	unreversible	JJ
cord-263987-ff6kor0c	79	24	aspects	aspect	NNS
cord-263987-ff6kor0c	79	25	of	of	IN
cord-263987-ff6kor0c	79	26	real	real	JJ
cord-263987-ff6kor0c	79	27	data	datum	NNS
cord-263987-ff6kor0c	79	28	,	,	,
cord-263987-ff6kor0c	79	29	limits	limit	VBZ
cord-263987-ff6kor0c	79	30	the	the	DT
cord-263987-ff6kor0c	79	31	expressiveness	expressiveness	NN
cord-263987-ff6kor0c	79	32	of	of	IN
cord-263987-ff6kor0c	79	33	the	the	DT
cord-263987-ff6kor0c	79	34	model	model	NN
cord-263987-ff6kor0c	79	35	,	,	,
cord-263987-ff6kor0c	79	36	and	and	CC
cord-263987-ff6kor0c	79	37	makes	make	VBZ
cord-263987-ff6kor0c	79	38	the	the	DT
cord-263987-ff6kor0c	79	39	root	root	NN
cord-263987-ff6kor0c	79	40	node	node	NN
cord-263987-ff6kor0c	79	41	placement	placement	NN
cord-263987-ff6kor0c	79	42	statistically	statistically	RB
cord-263987-ff6kor0c	79	43	unidentifiable	unidentifiable	JJ
cord-263987-ff6kor0c	79	44	.	.	.
cord-263987-ff6kor0c	80	1	Stationarity	stationarity	NN
cord-263987-ff6kor0c	80	2	has	have	VBZ
cord-263987-ff6kor0c	80	3	similar	similar	JJ
cord-263987-ff6kor0c	80	4	advantages	advantage	NNS
cord-263987-ff6kor0c	80	5	and	and	CC
cord-263987-ff6kor0c	80	6	drawbacks	drawback	NNS
cord-263987-ff6kor0c	80	7	.	.	.
cord-263987-ff6kor0c	81	1	If	if	IN
cord-263987-ff6kor0c	81	2	one	one	PRP
cord-263987-ff6kor0c	81	3	assumes	assume	VBZ
cord-263987-ff6kor0c	81	4	the	the	DT
cord-263987-ff6kor0c	81	5	process	process	NN
cord-263987-ff6kor0c	81	6	was	be	VBD
cord-263987-ff6kor0c	81	7	started	start	VBN
cord-263987-ff6kor0c	81	8	at	at	IN
cord-263987-ff6kor0c	81	9	equilibrium	equilibrium	NN
cord-263987-ff6kor0c	81	10	,	,	,
cord-263987-ff6kor0c	81	11	that	that	RB
cord-263987-ff6kor0c	81	12	is	be	VBZ
cord-263987-ff6kor0c	81	13	one	one	CD
cord-263987-ff6kor0c	81	14	less	less	JJR
cord-263987-ff6kor0c	81	15	set	set	NN
cord-263987-ff6kor0c	81	16	of	of	IN
cord-263987-ff6kor0c	81	17	parameters	parameter	NNS
cord-263987-ff6kor0c	81	18	to	to	TO
cord-263987-ff6kor0c	81	19	worry	worry	VB
cord-263987-ff6kor0c	81	20	about	about	IN
cord-263987-ff6kor0c	81	21	(	(	-LRB-
cord-263987-ff6kor0c	81	22	since	since	IN
cord-263987-ff6kor0c	81	23	the	the	DT
cord-263987-ff6kor0c	81	24	equilibrium	equilibrium	NN
cord-263987-ff6kor0c	81	25	distribution	distribution	NN
cord-263987-ff6kor0c	81	26	is	be	VBZ
cord-263987-ff6kor0c	81	27	implied	imply	VBN
cord-263987-ff6kor0c	81	28	by	by	IN
cord-263987-ff6kor0c	81	29	the	the	DT
cord-263987-ff6kor0c	81	30	process	process	NN
cord-263987-ff6kor0c	81	31	itself	-PRON-	PRP
cord-263987-ff6kor0c	81	32	)	)	-RRB-
cord-263987-ff6kor0c	81	33	,	,	,
cord-263987-ff6kor0c	81	34	but	but	CC
cord-263987-ff6kor0c	81	35	it	-PRON-	PRP
cord-263987-ff6kor0c	81	36	also	also	RB
cord-263987-ff6kor0c	81	37	renders	render	VBZ
cord-263987-ff6kor0c	81	38	the	the	DT
cord-263987-ff6kor0c	81	39	model	model	NN
cord-263987-ff6kor0c	81	40	less	less	RBR
cord-263987-ff6kor0c	81	41	expressive	expressive	JJ
cord-263987-ff6kor0c	81	42	and	and	CC
cord-263987-ff6kor0c	81	43	makes	make	VBZ
cord-263987-ff6kor0c	81	44	some	some	DT
cord-263987-ff6kor0c	81	45	kinds	kind	NNS
cord-263987-ff6kor0c	81	46	of	of	IN
cord-263987-ff6kor0c	81	47	inference	inference	NN
cord-263987-ff6kor0c	81	48	impossible	impossible	JJ
cord-263987-ff6kor0c	81	49	.	.	.
cord-263987-ff6kor0c	82	1	The	the	DT
cord-263987-ff6kor0c	82	2	early	early	JJ
cord-263987-ff6kor0c	82	3	literature	literature	NN
cord-263987-ff6kor0c	82	4	on	on	IN
cord-263987-ff6kor0c	82	5	substitution	substitution	NN
cord-263987-ff6kor0c	82	6	models	model	NNS
cord-263987-ff6kor0c	82	7	involved	involve	VBN
cord-263987-ff6kor0c	82	8	generalizing	generalize	VBG
cord-263987-ff6kor0c	82	9	from	from	IN
cord-263987-ff6kor0c	82	10	rate	rate	NN
cord-263987-ff6kor0c	82	11	matrices	matrix	NNS
cord-263987-ff6kor0c	82	12	R	r	NN
cord-263987-ff6kor0c	82	13	characterized	characterize	VBN
cord-263987-ff6kor0c	82	14	only	only	RB
cord-263987-ff6kor0c	82	15	by	by	IN
cord-263987-ff6kor0c	82	16	a	a	DT
cord-263987-ff6kor0c	82	17	single	single	JJ
cord-263987-ff6kor0c	82	18	rate	rate	NN
cord-263987-ff6kor0c	82	19	parameter	parameter	NN
cord-263987-ff6kor0c	82	20	[	[	-LRB-
cord-263987-ff6kor0c	82	21	1	1	CD
cord-263987-ff6kor0c	82	22	]	]	-RRB-
cord-263987-ff6kor0c	82	23	,	,	,
cord-263987-ff6kor0c	82	24	to	to	TO
cord-263987-ff6kor0c	82	25	symmetry	symmetry	VB
cord-263987-ff6kor0c	82	26	-	-	HYPH
cord-263987-ff6kor0c	82	27	breaking	break	VBG
cord-263987-ff6kor0c	82	28	versions	version	NNS
cord-263987-ff6kor0c	82	29	that	that	WDT
cord-263987-ff6kor0c	82	30	allowed	allow	VBD
cord-263987-ff6kor0c	82	31	for	for	IN
cord-263987-ff6kor0c	82	32	different	different	JJ
cord-263987-ff6kor0c	82	33	transition	transition	NN
cord-263987-ff6kor0c	82	34	and	and	CC
cord-263987-ff6kor0c	82	35	transversion	transversion	NN
cord-263987-ff6kor0c	82	36	rates	rate	NNS
cord-263987-ff6kor0c	82	37	[	[	-LRB-
cord-263987-ff6kor0c	82	38	31	31	CD
cord-263987-ff6kor0c	82	39	]	]	-RRB-
cord-263987-ff6kor0c	82	40	,	,	,
cord-263987-ff6kor0c	82	41	non	non	JJ
cord-263987-ff6kor0c	82	42	-	-	JJ
cord-263987-ff6kor0c	82	43	uniform	uniform	JJ
cord-263987-ff6kor0c	82	44	equilibrium	equilibrium	NN
cord-263987-ff6kor0c	82	45	distributions	distribution	NNS
cord-263987-ff6kor0c	82	46	over	over	IN
cord-263987-ff6kor0c	82	47	nucleotides	nucleotide	NNS
cord-263987-ff6kor0c	82	48	[	[	-LRB-
cord-263987-ff6kor0c	82	49	3	3	CD
cord-263987-ff6kor0c	82	50	]	]	-RRB-
cord-263987-ff6kor0c	82	51	,	,	,
cord-263987-ff6kor0c	82	52	and	and	CC
cord-263987-ff6kor0c	82	53	combinations	combination	NNS
cord-263987-ff6kor0c	82	54	of	of	IN
cord-263987-ff6kor0c	82	55	the	the	DT
cord-263987-ff6kor0c	82	56	above	above	JJ
cord-263987-ff6kor0c	82	57	[	[	-LRB-
cord-263987-ff6kor0c	82	58	32	32	CD
cord-263987-ff6kor0c	82	59	]	]	-RRB-
cord-263987-ff6kor0c	82	60	.	.	.
cord-263987-ff6kor0c	83	1	These	these	DT
cord-263987-ff6kor0c	83	2	models	model	NNS
cord-263987-ff6kor0c	83	3	are	be	VBP
cord-263987-ff6kor0c	83	4	all	all	DT
cord-263987-ff6kor0c	83	5	,	,	,
cord-263987-ff6kor0c	83	6	however	however	RB
cord-263987-ff6kor0c	83	7	,	,	,
cord-263987-ff6kor0c	83	8	reversible	reversible	JJ
cord-263987-ff6kor0c	83	9	.	.	.
cord-263987-ff6kor0c	84	1	A	a	DT
cord-263987-ff6kor0c	84	2	good	good	JJ
cord-263987-ff6kor0c	84	3	deal	deal	NN
cord-263987-ff6kor0c	84	4	of	of	IN
cord-263987-ff6kor0c	84	5	subsequent	subsequent	JJ
cord-263987-ff6kor0c	84	6	research	research	NN
cord-263987-ff6kor0c	84	7	has	have	VBZ
cord-263987-ff6kor0c	84	8	gone	go	VBN
cord-263987-ff6kor0c	84	9	into	into	IN
cord-263987-ff6kor0c	84	10	the	the	DT
cord-263987-ff6kor0c	84	11	problem	problem	NN
cord-263987-ff6kor0c	84	12	,	,	,
cord-263987-ff6kor0c	84	13	in	in	IN
cord-263987-ff6kor0c	84	14	various	various	JJ
cord-263987-ff6kor0c	84	15	guises	guise	NNS
cord-263987-ff6kor0c	84	16	,	,	,
cord-263987-ff6kor0c	84	17	of	of	IN
cord-263987-ff6kor0c	84	18	generalizing	generalize	VBG
cord-263987-ff6kor0c	84	19	results	result	NNS
cord-263987-ff6kor0c	84	20	obtained	obtain	VBN
cord-263987-ff6kor0c	84	21	for	for	IN
cord-263987-ff6kor0c	84	22	reversible	reversible	JJ
cord-263987-ff6kor0c	84	23	,	,	,
cord-263987-ff6kor0c	84	24	homogeneous	homogeneous	JJ
cord-263987-ff6kor0c	84	25	and/or	and/or	CC
cord-263987-ff6kor0c	84	26	stationary	stationary	JJ
cord-263987-ff6kor0c	84	27	models	model	NNS
cord-263987-ff6kor0c	84	28	to	to	IN
cord-263987-ff6kor0c	84	29	the	the	DT
cord-263987-ff6kor0c	84	30	analogous	analogous	JJ
cord-263987-ff6kor0c	84	31	irreversible	irreversible	JJ
cord-263987-ff6kor0c	84	32	,	,	,
cord-263987-ff6kor0c	84	33	nonhomogeneous	nonhomogeneous	JJ
cord-263987-ff6kor0c	84	34	and	and	CC
cord-263987-ff6kor0c	84	35	nonstationary	nonstationary	JJ
cord-263987-ff6kor0c	84	36	models	model	NNS
cord-263987-ff6kor0c	84	37	.	.	.
cord-263987-ff6kor0c	85	1	For	for	IN
cord-263987-ff6kor0c	85	2	examples	example	NNS
cord-263987-ff6kor0c	85	3	,	,	,
cord-263987-ff6kor0c	85	4	see	see	VB
cord-263987-ff6kor0c	85	5	[	[	-LRB-
cord-263987-ff6kor0c	85	6	30	30	CD
cord-263987-ff6kor0c	85	7	,	,	,
cord-263987-ff6kor0c	85	8	[	[	-LRB-
cord-263987-ff6kor0c	85	9	41	41	CD
cord-263987-ff6kor0c	85	10	]	]	-RRB-
cord-263987-ff6kor0c	85	11	[	[	-LRB-
cord-263987-ff6kor0c	85	12	42	42	CD
cord-263987-ff6kor0c	85	13	]	]	-RRB-
cord-263987-ff6kor0c	85	14	[	[	-LRB-
cord-263987-ff6kor0c	85	15	43	43	CD
cord-263987-ff6kor0c	85	16	]	]	-RRB-
cord-263987-ff6kor0c	85	17	.	.	.
cord-263987-ff6kor0c	86	1	The	the	DT
cord-263987-ff6kor0c	86	2	question	question	NN
cord-263987-ff6kor0c	86	3	naturally	naturally	RB
cord-263987-ff6kor0c	86	4	arises	arise	VBZ
cord-263987-ff6kor0c	86	5	:	:	:
cord-263987-ff6kor0c	86	6	how	how	WRB
cord-263987-ff6kor0c	86	7	to	to	TO
cord-263987-ff6kor0c	86	8	extend	extend	VB
cord-263987-ff6kor0c	86	9	the	the	DT
cord-263987-ff6kor0c	86	10	model	model	NN
cord-263987-ff6kor0c	86	11	to	to	TO
cord-263987-ff6kor0c	86	12	describe	describe	VB
cord-263987-ff6kor0c	86	13	the	the	DT
cord-263987-ff6kor0c	86	14	evolution	evolution	NN
cord-263987-ff6kor0c	86	15	of	of	IN
cord-263987-ff6kor0c	86	16	an	an	DT
cord-263987-ff6kor0c	86	17	entire	entire	JJ
cord-263987-ff6kor0c	86	18	sequence	sequence	NN
cord-263987-ff6kor0c	86	19	,	,	,
cord-263987-ff6kor0c	86	20	not	not	RB
cord-263987-ff6kor0c	86	21	just	just	RB
cord-263987-ff6kor0c	86	22	individual	individual	JJ
cord-263987-ff6kor0c	86	23	sites	site	NNS
cord-263987-ff6kor0c	86	24	?	?	.
cord-263987-ff6kor0c	87	1	In	in	IN
cord-263987-ff6kor0c	87	2	such	such	JJ
cord-263987-ff6kor0c	87	3	cases	case	NNS
cord-263987-ff6kor0c	87	4	,	,	,
cord-263987-ff6kor0c	87	5	when	when	WRB
cord-263987-ff6kor0c	87	6	one	one	CD
cord-263987-ff6kor0c	87	7	talks	talk	VBZ
cord-263987-ff6kor0c	87	8	about	about	IN
cord-263987-ff6kor0c	87	9	M(t	M(t	NNS
cord-263987-ff6kor0c	87	10	)	)	-RRB-
cord-263987-ff6kor0c	88	1	i	i	PRP
cord-263987-ff6kor0c	88	2	,	,	,
cord-263987-ff6kor0c	88	3	j	j	NNP
cord-263987-ff6kor0c	88	4	"	"	``
cord-263987-ff6kor0c	88	5	the	the	DT
cord-263987-ff6kor0c	88	6	likelihood	likelihood	NN
cord-263987-ff6kor0c	88	7	of	of	IN
cord-263987-ff6kor0c	88	8	an	an	DT
cord-263987-ff6kor0c	88	9	ancestor	ancestor	NN
cord-263987-ff6kor0c	88	10	-	-	HYPH
cord-263987-ff6kor0c	88	11	descendant	descendant	JJ
cord-263987-ff6kor0c	88	12	pair	pair	NN
cord-263987-ff6kor0c	88	13	(	(	-LRB-
cord-263987-ff6kor0c	88	14	i	i	NN
cord-263987-ff6kor0c	88	15	,	,	,
cord-263987-ff6kor0c	88	16	j	j	NNP
cord-263987-ff6kor0c	88	17	)	)	-RRB-
cord-263987-ff6kor0c	88	18	"	"	''
cord-263987-ff6kor0c	89	1	(	(	-LRB-
cord-263987-ff6kor0c	89	2	or	or	CC
cord-263987-ff6kor0c	89	3	,	,	,
cord-263987-ff6kor0c	89	4	more	more	RBR
cord-263987-ff6kor0c	89	5	precisely	precisely	RB
cord-263987-ff6kor0c	89	6	,	,	,
cord-263987-ff6kor0c	89	7	the	the	DT
cord-263987-ff6kor0c	89	8	probability	probability	NN
cord-263987-ff6kor0c	89	9	that	that	WDT
cord-263987-ff6kor0c	89	10	-	-	HYPH
cord-263987-ff6kor0c	89	11	given	give	VBN
cord-263987-ff6kor0c	89	12	the	the	DT
cord-263987-ff6kor0c	89	13	system	system	NN
cord-263987-ff6kor0c	89	14	starts	start	VBZ
cord-263987-ff6kor0c	89	15	in	in	IN
cord-263987-ff6kor0c	89	16	ancestral	ancestral	JJ
cord-263987-ff6kor0c	89	17	state	state	NN
cord-263987-ff6kor0c	89	18	i	i	PRP
cord-263987-ff6kor0c	89	19	-	-	:
cord-263987-ff6kor0c	89	20	it	-PRON-	PRP
cord-263987-ff6kor0c	89	21	will	will	MD
cord-263987-ff6kor0c	89	22	after	after	IN
cord-263987-ff6kor0c	89	23	time	time	NN
cord-263987-ff6kor0c	89	24	t	t	NNP
cord-263987-ff6kor0c	89	25	have	have	VBP
cord-263987-ff6kor0c	89	26	evolved	evolve	VBN
cord-263987-ff6kor0c	89	27	into	into	IN
cord-263987-ff6kor0c	89	28	descendant	descendant	JJ
cord-263987-ff6kor0c	89	29	state	state	NN
cord-263987-ff6kor0c	89	30	j	j	NNP
cord-263987-ff6kor0c	89	31	)	)	-RRB-
cord-263987-ff6kor0c	90	1	one	one	PRP
cord-263987-ff6kor0c	90	2	must	must	MD
cord-263987-ff6kor0c	90	3	bear	bear	VB
cord-263987-ff6kor0c	90	4	in	in	IN
cord-263987-ff6kor0c	90	5	mind	mind	NN
cord-263987-ff6kor0c	90	6	that	that	IN
cord-263987-ff6kor0c	90	7	the	the	DT
cord-263987-ff6kor0c	90	8	states	state	NNS
cord-263987-ff6kor0c	91	1	i	i	PRP
cord-263987-ff6kor0c	91	2	and	and	CC
cord-263987-ff6kor0c	91	3	j	j	NNP
cord-263987-ff6kor0c	91	4	now	now	RB
cord-263987-ff6kor0c	91	5	represent	represent	VBP
cord-263987-ff6kor0c	91	6	not	not	RB
cord-263987-ff6kor0c	91	7	just	just	RB
cord-263987-ff6kor0c	91	8	individual	individual	JJ
cord-263987-ff6kor0c	91	9	residues	residue	NNS
cord-263987-ff6kor0c	91	10	,	,	,
cord-263987-ff6kor0c	91	11	but	but	CC
cord-263987-ff6kor0c	91	12	entire	entire	JJ
cord-263987-ff6kor0c	91	13	sequences	sequence	NNS
cord-263987-ff6kor0c	91	14	.	.	.
cord-263987-ff6kor0c	92	1	As	as	RB
cord-263987-ff6kor0c	92	2	long	long	RB
cord-263987-ff6kor0c	92	3	as	as	IN
cord-263987-ff6kor0c	92	4	the	the	DT
cord-263987-ff6kor0c	92	5	allowed	allow	VBN
cord-263987-ff6kor0c	92	6	mutations	mutation	NNS
cord-263987-ff6kor0c	92	7	are	be	VBP
cord-263987-ff6kor0c	92	8	restricted	restrict	VBN
cord-263987-ff6kor0c	92	9	to	to	IN
cord-263987-ff6kor0c	92	10	point	point	NN
cord-263987-ff6kor0c	92	11	substitutions	substitution	NNS
cord-263987-ff6kor0c	92	12	and	and	CC
cord-263987-ff6kor0c	92	13	their	-PRON-	PRP$
cord-263987-ff6kor0c	92	14	mutation	mutation	NN
cord-263987-ff6kor0c	92	15	rates	rate	NNS
cord-263987-ff6kor0c	92	16	are	be	VBP
cord-263987-ff6kor0c	92	17	independent	independent	JJ
cord-263987-ff6kor0c	92	18	of	of	IN
cord-263987-ff6kor0c	92	19	flanking	flanking	JJ
cord-263987-ff6kor0c	92	20	context	context	NN
cord-263987-ff6kor0c	92	21	,	,	,
cord-263987-ff6kor0c	92	22	then	then	RB
cord-263987-ff6kor0c	92	23	the	the	DT
cord-263987-ff6kor0c	92	24	extension	extension	NN
cord-263987-ff6kor0c	92	25	to	to	IN
cord-263987-ff6kor0c	92	26	whole	whole	JJ
cord-263987-ff6kor0c	92	27	sequences	sequence	NNS
cord-263987-ff6kor0c	92	28	is	be	VBZ
cord-263987-ff6kor0c	92	29	trivially	trivially	RB
cord-263987-ff6kor0c	92	30	easy	easy	JJ
cord-263987-ff6kor0c	92	31	:	:	:
cord-263987-ff6kor0c	92	32	one	one	PRP
cord-263987-ff6kor0c	92	33	can	can	MD
cord-263987-ff6kor0c	92	34	simply	simply	RB
cord-263987-ff6kor0c	92	35	multiply	multiply	VB
cord-263987-ff6kor0c	92	36	together	together	RB
cord-263987-ff6kor0c	92	37	probabilities	probability	NNS
cord-263987-ff6kor0c	92	38	of	of	IN
cord-263987-ff6kor0c	92	39	independent	independent	JJ
cord-263987-ff6kor0c	92	40	sites	site	NNS
cord-263987-ff6kor0c	92	41	.	.	.
cord-263987-ff6kor0c	93	1	However	however	RB
cord-263987-ff6kor0c	93	2	,	,	,
cord-263987-ff6kor0c	93	3	many	many	JJ
cord-263987-ff6kor0c	93	4	kinds	kind	NNS
cord-263987-ff6kor0c	93	5	of	of	IN
cord-263987-ff6kor0c	93	6	mutation	mutation	NN
cord-263987-ff6kor0c	93	7	violate	violate	VBP
cord-263987-ff6kor0c	93	8	this	this	DT
cord-263987-ff6kor0c	93	9	assumption	assumption	NN
cord-263987-ff6kor0c	93	10	of	of	IN
cord-263987-ff6kor0c	93	11	site	site	NN
cord-263987-ff6kor0c	93	12	independence	independence	NN
cord-263987-ff6kor0c	93	13	;	;	:
cord-263987-ff6kor0c	93	14	most	most	RBS
cord-263987-ff6kor0c	93	15	notably	notably	RB
cord-263987-ff6kor0c	93	16	contextdependent	contextdependent	JJ
cord-263987-ff6kor0c	93	17	substitutions	substitution	NNS
cord-263987-ff6kor0c	93	18	and	and	CC
cord-263987-ff6kor0c	93	19	indels	indel	NNS
cord-263987-ff6kor0c	93	20	,	,	,
cord-263987-ff6kor0c	93	21	where	where	WRB
cord-263987-ff6kor0c	93	22	the	the	DT
cord-263987-ff6kor0c	93	23	rates	rate	NNS
cord-263987-ff6kor0c	93	24	depend	depend	VBP
cord-263987-ff6kor0c	93	25	on	on	IN
cord-263987-ff6kor0c	93	26	neighboring	neighboring	NN
cord-263987-ff6kor0c	93	27	sites	site	NNS
cord-263987-ff6kor0c	93	28	.	.	.
cord-263987-ff6kor0c	94	1	For	for	IN
cord-263987-ff6kor0c	94	2	these	these	DT
cord-263987-ff6kor0c	94	3	mutations	mutation	NNS
cord-263987-ff6kor0c	94	4	the	the	DT
cord-263987-ff6kor0c	94	5	natural	natural	JJ
cord-263987-ff6kor0c	94	6	approach	approach	NN
cord-263987-ff6kor0c	94	7	is	be	VBZ
cord-263987-ff6kor0c	94	8	to	to	TO
cord-263987-ff6kor0c	94	9	extend	extend	VB
cord-263987-ff6kor0c	94	10	the	the	DT
cord-263987-ff6kor0c	94	11	state	state	NN
cord-263987-ff6kor0c	94	12	space	space	NN
cord-263987-ff6kor0c	94	13	to	to	TO
cord-263987-ff6kor0c	94	14	be	be	VB
cord-263987-ff6kor0c	94	15	the	the	DT
cord-263987-ff6kor0c	94	16	set	set	NN
cord-263987-ff6kor0c	94	17	of	of	IN
cord-263987-ff6kor0c	94	18	all	all	DT
cord-263987-ff6kor0c	94	19	possible	possible	JJ
cord-263987-ff6kor0c	94	20	sequences	sequence	NNS
cord-263987-ff6kor0c	94	21	over	over	IN
cord-263987-ff6kor0c	94	22	a	a	DT
cord-263987-ff6kor0c	94	23	given	give	VBN
cord-263987-ff6kor0c	94	24	alphabet	alphabet	NN
cord-263987-ff6kor0c	94	25	(	(	-LRB-
cord-263987-ff6kor0c	94	26	for	for	IN
cord-263987-ff6kor0c	94	27	example	example	NN
cord-263987-ff6kor0c	94	28	,	,	,
cord-263987-ff6kor0c	94	29	the	the	DT
cord-263987-ff6kor0c	94	30	set	set	NN
cord-263987-ff6kor0c	94	31	of	of	IN
cord-263987-ff6kor0c	94	32	all	all	DT
cord-263987-ff6kor0c	94	33	DNA	dna	NN
cord-263987-ff6kor0c	94	34	or	or	CC
cord-263987-ff6kor0c	94	35	protein	protein	NN
cord-263987-ff6kor0c	94	36	sequences	sequence	NNS
cord-263987-ff6kor0c	94	37	)	)	-RRB-
cord-263987-ff6kor0c	94	38	.	.	.
cord-263987-ff6kor0c	95	1	This	this	DT
cord-263987-ff6kor0c	95	2	state	state	NN
cord-263987-ff6kor0c	95	3	space	space	NN
cord-263987-ff6kor0c	95	4	is	be	VBZ
cord-263987-ff6kor0c	95	5	(	(	-LRB-
cord-263987-ff6kor0c	95	6	countably	countably	RB
cord-263987-ff6kor0c	95	7	)	)	-RRB-
cord-263987-ff6kor0c	95	8	infinite	infinite	JJ
cord-263987-ff6kor0c	95	9	;	;	:
cord-263987-ff6kor0c	95	10	Eqs	Eqs	NNP
cord-263987-ff6kor0c	95	11	.	.	.
cord-263987-ff6kor0c	96	1	1	1	LS
cord-263987-ff6kor0c	96	2	-	-	SYM
cord-263987-ff6kor0c	96	3	4	4	CD
cord-263987-ff6kor0c	96	4	can	can	MD
cord-263987-ff6kor0c	96	5	still	still	RB
cord-263987-ff6kor0c	96	6	be	be	VB
cord-263987-ff6kor0c	96	7	used	use	VBN
cord-263987-ff6kor0c	96	8	on	on	IN
cord-263987-ff6kor0c	96	9	an	an	DT
cord-263987-ff6kor0c	96	10	infinite	infinite	JJ
cord-263987-ff6kor0c	96	11	state	state	NN
cord-263987-ff6kor0c	96	12	space	space	NN
cord-263987-ff6kor0c	96	13	,	,	,
cord-263987-ff6kor0c	96	14	but	but	CC
cord-263987-ff6kor0c	96	15	solution	solution	NN
cord-263987-ff6kor0c	96	16	by	by	IN
cord-263987-ff6kor0c	96	17	brute	brute	JJ
cord-263987-ff6kor0c	96	18	-	-	HYPH
cord-263987-ff6kor0c	96	19	force	force	NN
cord-263987-ff6kor0c	96	20	enumeration	enumeration	NN
cord-263987-ff6kor0c	96	21	of	of	IN
cord-263987-ff6kor0c	96	22	eigenvalues	eigenvalue	NNS
cord-263987-ff6kor0c	96	23	and	and	CC
cord-263987-ff6kor0c	96	24	eigenvectors	eigenvector	NNS
cord-263987-ff6kor0c	96	25	is	be	VBZ
cord-263987-ff6kor0c	96	26	no	no	DT
cord-263987-ff6kor0c	96	27	longer	long	RBR
cord-263987-ff6kor0c	96	28	feasible	feasible	JJ
cord-263987-ff6kor0c	96	29	,	,	,
cord-263987-ff6kor0c	96	30	except	except	IN
cord-263987-ff6kor0c	96	31	in	in	IN
cord-263987-ff6kor0c	96	32	special	special	JJ
cord-263987-ff6kor0c	96	33	cases	case	NNS
cord-263987-ff6kor0c	96	34	where	where	WRB
cord-263987-ff6kor0c	96	35	there	there	EX
cord-263987-ff6kor0c	96	36	is	be	VBZ
cord-263987-ff6kor0c	96	37	explicit	explicit	JJ
cord-263987-ff6kor0c	96	38	structure	structure	NN
cord-263987-ff6kor0c	96	39	to	to	IN
cord-263987-ff6kor0c	96	40	the	the	DT
cord-263987-ff6kor0c	96	41	rate	rate	NN
cord-263987-ff6kor0c	96	42	matrix	matrix	NN
cord-263987-ff6kor0c	96	43	that	that	WDT
cord-263987-ff6kor0c	96	44	allows	allow	VBZ
cord-263987-ff6kor0c	96	45	identification	identification	NN
cord-263987-ff6kor0c	96	46	of	of	IN
cord-263987-ff6kor0c	96	47	the	the	DT
cord-263987-ff6kor0c	96	48	eigensystem	eigensystem	NN
cord-263987-ff6kor0c	96	49	by	by	IN
cord-263987-ff6kor0c	96	50	algebraic	algebraic	JJ
cord-263987-ff6kor0c	96	51	approaches	approach	NNS
cord-263987-ff6kor0c	96	52	[	[	-LRB-
cord-263987-ff6kor0c	96	53	44	44	CD
cord-263987-ff6kor0c	96	54	,	,	,
cord-263987-ff6kor0c	96	55	45	45	CD
cord-263987-ff6kor0c	96	56	]	]	-RRB-
cord-263987-ff6kor0c	96	57	.	.	.
cord-263987-ff6kor0c	97	1	It	-PRON-	PRP
cord-263987-ff6kor0c	97	2	has	have	VBZ
cord-263987-ff6kor0c	97	3	turned	turn	VBN
cord-263987-ff6kor0c	97	4	out	out	RP
cord-263987-ff6kor0c	97	5	that	that	IN
cord-263987-ff6kor0c	97	6	whole	whole	JJ
cord-263987-ff6kor0c	97	7	-	-	HYPH
cord-263987-ff6kor0c	97	8	sequence	sequence	NN
cord-263987-ff6kor0c	97	9	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	97	10	models	model	NNS
cord-263987-ff6kor0c	97	11	have	have	VBP
cord-263987-ff6kor0c	97	12	proved	prove	VBN
cord-263987-ff6kor0c	97	13	quite	quite	RB
cord-263987-ff6kor0c	97	14	challenging	challenging	JJ
cord-263987-ff6kor0c	97	15	for	for	IN
cord-263987-ff6kor0c	97	16	theorists	theorist	NNS
cord-263987-ff6kor0c	97	17	.	.	.
cord-263987-ff6kor0c	98	1	There	there	EX
cord-263987-ff6kor0c	98	2	is	be	VBZ
cord-263987-ff6kor0c	98	3	extensive	extensive	JJ
cord-263987-ff6kor0c	98	4	evidence	evidence	NN
cord-263987-ff6kor0c	98	5	suggesting	suggest	VBG
cord-263987-ff6kor0c	98	6	that	that	IN
cord-263987-ff6kor0c	98	7	indels	indel	NNS
cord-263987-ff6kor0c	98	8	,	,	,
cord-263987-ff6kor0c	98	9	in	in	IN
cord-263987-ff6kor0c	98	10	particular	particular	JJ
cord-263987-ff6kor0c	98	11	,	,	,
cord-263987-ff6kor0c	98	12	can	can	MD
cord-263987-ff6kor0c	98	13	be	be	VB
cord-263987-ff6kor0c	98	14	profoundly	profoundly	RB
cord-263987-ff6kor0c	98	15	informative	informative	JJ
cord-263987-ff6kor0c	98	16	to	to	IN
cord-263987-ff6kor0c	98	17	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	98	18	studies	study	NNS
cord-263987-ff6kor0c	98	19	,	,	,
cord-263987-ff6kor0c	98	20	and	and	CC
cord-263987-ff6kor0c	98	21	to	to	IN
cord-263987-ff6kor0c	98	22	applications	application	NNS
cord-263987-ff6kor0c	98	23	of	of	IN
cord-263987-ff6kor0c	98	24	phylogenetics	phylogenetic	NNS
cord-263987-ff6kor0c	98	25	in	in	IN
cord-263987-ff6kor0c	98	26	sequence	sequence	NN
cord-263987-ff6kor0c	98	27	analysis	analysis	NN
cord-263987-ff6kor0c	98	28	[	[	-LRB-
cord-263987-ff6kor0c	98	29	46	46	CD
cord-263987-ff6kor0c	98	30	]	]	-RRB-
cord-263987-ff6kor0c	99	1	[	[	-LRB-
cord-263987-ff6kor0c	99	2	47	47	CD
cord-263987-ff6kor0c	99	3	]	]	-RRB-
cord-263987-ff6kor0c	100	1	[	[	-LRB-
cord-263987-ff6kor0c	100	2	48	48	CD
cord-263987-ff6kor0c	100	3	]	]	-RRB-
cord-263987-ff6kor0c	101	1	[	[	-LRB-
cord-263987-ff6kor0c	101	2	49	49	CD
cord-263987-ff6kor0c	101	3	]	]	-RRB-
cord-263987-ff6kor0c	101	4	[	[	-LRB-
cord-263987-ff6kor0c	101	5	50	50	CD
cord-263987-ff6kor0c	101	6	]	]	-RRB-
cord-263987-ff6kor0c	101	7	[	[	-LRB-
cord-263987-ff6kor0c	101	8	51	51	CD
cord-263987-ff6kor0c	101	9	]	]	-RRB-
cord-263987-ff6kor0c	101	10	.	.	.
cord-263987-ff6kor0c	102	1	The	the	DT
cord-263987-ff6kor0c	102	2	field	field	NN
cord-263987-ff6kor0c	102	3	of	of	IN
cord-263987-ff6kor0c	102	4	efforts	effort	NNS
cord-263987-ff6kor0c	102	5	to	to	TO
cord-263987-ff6kor0c	102	6	unify	unify	VB
cord-263987-ff6kor0c	102	7	alignment	alignment	NN
cord-263987-ff6kor0c	102	8	and	and	CC
cord-263987-ff6kor0c	102	9	phylogeny	phylogeny	NN
cord-263987-ff6kor0c	102	10	,	,	,
cord-263987-ff6kor0c	102	11	and	and	CC
cord-263987-ff6kor0c	102	12	to	to	TO
cord-263987-ff6kor0c	102	13	build	build	VB
cord-263987-ff6kor0c	102	14	a	a	DT
cord-263987-ff6kor0c	102	15	theoretical	theoretical	JJ
cord-263987-ff6kor0c	102	16	framework	framework	NN
cord-263987-ff6kor0c	102	17	for	for	IN
cord-263987-ff6kor0c	102	18	the	the	DT
cord-263987-ff6kor0c	102	19	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	102	20	analysis	analysis	NN
cord-263987-ff6kor0c	102	21	of	of	IN
cord-263987-ff6kor0c	102	22	indels	indel	NNS
cord-263987-ff6kor0c	102	23	,	,	,
cord-263987-ff6kor0c	102	24	has	have	VBZ
cord-263987-ff6kor0c	102	25	been	be	VBN
cord-263987-ff6kor0c	102	26	dubbed	dub	VBN
cord-263987-ff6kor0c	102	27	statistical	statistical	JJ
cord-263987-ff6kor0c	102	28	alignment	alignment	NN
cord-263987-ff6kor0c	102	29	by	by	IN
cord-263987-ff6kor0c	102	30	Hein	Hein	NNP
cord-263987-ff6kor0c	102	31	,	,	,
cord-263987-ff6kor0c	102	32	one	one	CD
cord-263987-ff6kor0c	102	33	of	of	IN
cord-263987-ff6kor0c	102	34	its	-PRON-	PRP$
cord-263987-ff6kor0c	102	35	pioneers	pioneer	NNS
cord-263987-ff6kor0c	102	36	[	[	-LRB-
cord-263987-ff6kor0c	102	37	52	52	CD
cord-263987-ff6kor0c	102	38	]	]	-RRB-
cord-263987-ff6kor0c	102	39	.	.	.
cord-263987-ff6kor0c	103	1	Recent	recent	JJ
cord-263987-ff6kor0c	103	2	publications	publication	NNS
cord-263987-ff6kor0c	103	3	by	by	IN
cord-263987-ff6kor0c	103	4	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	103	5	[	[	-LRB-
cord-263987-ff6kor0c	103	6	53	53	CD
cord-263987-ff6kor0c	103	7	]	]	-RRB-
cord-263987-ff6kor0c	103	8	[	[	-LRB-
cord-263987-ff6kor0c	103	9	54	54	CD
cord-263987-ff6kor0c	103	10	]	]	-RRB-
cord-263987-ff6kor0c	103	11	[	[	-LRB-
cord-263987-ff6kor0c	103	12	55	55	CD
cord-263987-ff6kor0c	103	13	]	]	-RRB-
cord-263987-ff6kor0c	103	14	and	and	CC
cord-263987-ff6kor0c	103	15	Rivas	Rivas	NNP
cord-263987-ff6kor0c	103	16	and	and	CC
cord-263987-ff6kor0c	103	17	Eddy	Eddy	NNP
cord-263987-ff6kor0c	103	18	[	[	-LRB-
cord-263987-ff6kor0c	103	19	56	56	CD
cord-263987-ff6kor0c	103	20	]	]	-RRB-
cord-263987-ff6kor0c	103	21	have	have	VBP
cord-263987-ff6kor0c	103	22	highlighted	highlight	VBN
cord-263987-ff6kor0c	103	23	this	this	DT
cord-263987-ff6kor0c	103	24	problem	problem	NN
cord-263987-ff6kor0c	103	25	once	once	RB
cord-263987-ff6kor0c	103	26	again	again	RB
cord-263987-ff6kor0c	103	27	,	,	,
cord-263987-ff6kor0c	103	28	directly	directly	RB
cord-263987-ff6kor0c	103	29	leading	lead	VBG
cord-263987-ff6kor0c	103	30	to	to	IN
cord-263987-ff6kor0c	103	31	the	the	DT
cord-263987-ff6kor0c	103	32	present	present	JJ
cord-263987-ff6kor0c	103	33	review	review	NN
cord-263987-ff6kor0c	103	34	.	.	.
cord-263987-ff6kor0c	104	1	In	in	IN
cord-263987-ff6kor0c	104	2	this	this	DT
cord-263987-ff6kor0c	104	3	paper	paper	NN
cord-263987-ff6kor0c	104	4	I	-PRON-	PRP
cord-263987-ff6kor0c	104	5	focus	focus	VBP
cord-263987-ff6kor0c	104	6	only	only	RB
cord-263987-ff6kor0c	104	7	on	on	IN
cord-263987-ff6kor0c	104	8	"	"	``
cord-263987-ff6kor0c	104	9	local	local	JJ
cord-263987-ff6kor0c	104	10	"	"	''
cord-263987-ff6kor0c	104	11	mutations	mutation	NNS
cord-263987-ff6kor0c	104	12	:	:	:
cord-263987-ff6kor0c	104	13	mostly	mostly	RB
cord-263987-ff6kor0c	104	14	indel	indel	JJ
cord-263987-ff6kor0c	104	15	events	event	NNS
cord-263987-ff6kor0c	104	16	(	(	-LRB-
cord-263987-ff6kor0c	104	17	which	which	WDT
cord-263987-ff6kor0c	104	18	may	may	MD
cord-263987-ff6kor0c	104	19	include	include	VB
cord-263987-ff6kor0c	104	20	local	local	JJ
cord-263987-ff6kor0c	104	21	duplications	duplication	NNS
cord-263987-ff6kor0c	104	22	)	)	-RRB-
cord-263987-ff6kor0c	104	23	,	,	,
cord-263987-ff6kor0c	104	24	but	but	CC
cord-263987-ff6kor0c	104	25	also	also	RB
cord-263987-ff6kor0c	104	26	context	context	NN
cord-263987-ff6kor0c	104	27	-	-	HYPH
cord-263987-ff6kor0c	104	28	dependent	dependent	JJ
cord-263987-ff6kor0c	104	29	substitutions	substitution	NNS
cord-263987-ff6kor0c	104	30	.	.	.
cord-263987-ff6kor0c	105	1	This	this	DT
cord-263987-ff6kor0c	105	2	is	be	VBZ
cord-263987-ff6kor0c	105	3	not	not	RB
cord-263987-ff6kor0c	105	4	because	because	IN
cord-263987-ff6kor0c	105	5	"	"	``
cord-263987-ff6kor0c	105	6	nonlocal	nonlocal	JJ
cord-263987-ff6kor0c	105	7	"	"	''
cord-263987-ff6kor0c	105	8	events	event	NNS
cord-263987-ff6kor0c	105	9	(	(	-LRB-
cord-263987-ff6kor0c	105	10	such	such	JJ
cord-263987-ff6kor0c	105	11	as	as	IN
cord-263987-ff6kor0c	105	12	rearrangements	rearrangement	NNS
cord-263987-ff6kor0c	105	13	)	)	-RRB-
cord-263987-ff6kor0c	105	14	are	be	VBP
cord-263987-ff6kor0c	105	15	unimportant	unimportant	JJ
cord-263987-ff6kor0c	105	16	,	,	,
cord-263987-ff6kor0c	105	17	but	but	CC
cord-263987-ff6kor0c	105	18	rather	rather	RB
cord-263987-ff6kor0c	105	19	that	that	IN
cord-263987-ff6kor0c	105	20	they	-PRON-	PRP
cord-263987-ff6kor0c	105	21	tend	tend	VBP
cord-263987-ff6kor0c	105	22	to	to	TO
cord-263987-ff6kor0c	105	23	defy	defy	VB
cord-263987-ff6kor0c	105	24	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	105	25	reconstruction	reconstruction	NN
cord-263987-ff6kor0c	105	26	due	due	IN
cord-263987-ff6kor0c	105	27	to	to	IN
cord-263987-ff6kor0c	105	28	the	the	DT
cord-263987-ff6kor0c	105	29	rapid	rapid	JJ
cord-263987-ff6kor0c	105	30	proliferation	proliferation	NN
cord-263987-ff6kor0c	105	31	of	of	IN
cord-263987-ff6kor0c	105	32	possible	possible	JJ
cord-263987-ff6kor0c	105	33	histories	history	NNS
cord-263987-ff6kor0c	105	34	after	after	IN
cord-263987-ff6kor0c	105	35	even	even	RB
cord-263987-ff6kor0c	105	36	a	a	DT
cord-263987-ff6kor0c	105	37	few	few	JJ
cord-263987-ff6kor0c	105	38	such	such	JJ
cord-263987-ff6kor0c	105	39	events	event	NNS
cord-263987-ff6kor0c	105	40	[	[	-LRB-
cord-263987-ff6kor0c	105	41	57	57	CD
cord-263987-ff6kor0c	105	42	]	]	-RRB-
cord-263987-ff6kor0c	105	43	.	.	.
cord-263987-ff6kor0c	106	1	The	the	DT
cord-263987-ff6kor0c	106	2	discussion	discussion	NN
cord-263987-ff6kor0c	106	3	here	here	RB
cord-263987-ff6kor0c	106	4	is	be	VBZ
cord-263987-ff6kor0c	106	5	separated	separate	VBN
cord-263987-ff6kor0c	106	6	into	into	IN
cord-263987-ff6kor0c	106	7	two	two	CD
cord-263987-ff6kor0c	106	8	parts	part	NNS
cord-263987-ff6kor0c	106	9	.	.	.
cord-263987-ff6kor0c	107	1	In	in	IN
cord-263987-ff6kor0c	107	2	the	the	DT
cord-263987-ff6kor0c	107	3	first	first	JJ
cord-263987-ff6kor0c	107	4	part	part	NN
cord-263987-ff6kor0c	107	5	,	,	,
cord-263987-ff6kor0c	107	6	I	-PRON-	PRP
cord-263987-ff6kor0c	107	7	discuss	discuss	VBP
cord-263987-ff6kor0c	107	8	the	the	DT
cord-263987-ff6kor0c	107	9	master	master	NN
cord-263987-ff6kor0c	107	10	equation	equation	NN
cord-263987-ff6kor0c	107	11	(	(	-LRB-
cord-263987-ff6kor0c	107	12	Eq	Eq	NNP
cord-263987-ff6kor0c	107	13	.	.	NNP
cord-263987-ff6kor0c	107	14	1	1	CD
cord-263987-ff6kor0c	107	15	)	)	-RRB-
cord-263987-ff6kor0c	107	16	and	and	CC
cord-263987-ff6kor0c	107	17	exact	exact	JJ
cord-263987-ff6kor0c	107	18	solutions	solution	NNS
cord-263987-ff6kor0c	107	19	thereof	thereof	RB
cord-263987-ff6kor0c	108	1	(	(	-LRB-
cord-263987-ff6kor0c	108	2	Eq	Eq	NNP
cord-263987-ff6kor0c	108	3	.	.	NNP
cord-263987-ff6kor0c	108	4	2	2	CD
cord-263987-ff6kor0c	108	5	)	)	-RRB-
cord-263987-ff6kor0c	108	6	,	,	,
cord-263987-ff6kor0c	108	7	along	along	IN
cord-263987-ff6kor0c	108	8	with	with	IN
cord-263987-ff6kor0c	108	9	various	various	JJ
cord-263987-ff6kor0c	108	10	approximations	approximation	NNS
cord-263987-ff6kor0c	108	11	and	and	CC
cord-263987-ff6kor0c	108	12	their	-PRON-	PRP$
cord-263987-ff6kor0c	108	13	departure	departure	NN
cord-263987-ff6kor0c	108	14	from	from	IN
cord-263987-ff6kor0c	108	15	the	the	DT
cord-263987-ff6kor0c	108	16	Chapman	Chapman	NNP
cord-263987-ff6kor0c	108	17	-	-	HYPH
cord-263987-ff6kor0c	108	18	Kolmogorov	Kolmogorov	NNP
cord-263987-ff6kor0c	108	19	ideal	ideal	NN
cord-263987-ff6kor0c	108	20	(	(	-LRB-
cord-263987-ff6kor0c	108	21	Eq	Eq	NNP
cord-263987-ff6kor0c	108	22	.	.	NNP
cord-263987-ff6kor0c	108	23	3	3	CD
cord-263987-ff6kor0c	108	24	)	)	-RRB-
cord-263987-ff6kor0c	108	25	.	.	.
cord-263987-ff6kor0c	109	1	This	this	DT
cord-263987-ff6kor0c	109	2	is	be	VBZ
cord-263987-ff6kor0c	109	3	an	an	DT
cord-263987-ff6kor0c	109	4	area	area	NN
cord-263987-ff6kor0c	109	5	in	in	IN
cord-263987-ff6kor0c	109	6	which	which	WDT
cord-263987-ff6kor0c	109	7	recent	recent	JJ
cord-263987-ff6kor0c	109	8	progress	progress	NN
cord-263987-ff6kor0c	109	9	has	have	VBZ
cord-263987-ff6kor0c	109	10	been	be	VBN
cord-263987-ff6kor0c	109	11	reported	report	VBN
cord-263987-ff6kor0c	109	12	in	in	IN
cord-263987-ff6kor0c	109	13	this	this	DT
cord-263987-ff6kor0c	109	14	journal	journal	NN
cord-263987-ff6kor0c	109	15	.	.	.
cord-263987-ff6kor0c	110	1	In	in	IN
cord-263987-ff6kor0c	110	2	the	the	DT
cord-263987-ff6kor0c	110	3	second	second	JJ
cord-263987-ff6kor0c	110	4	part	part	NN
cord-263987-ff6kor0c	110	5	,	,	,
cord-263987-ff6kor0c	110	6	I	-PRON-	PRP
cord-263987-ff6kor0c	110	7	review	review	VBP
cord-263987-ff6kor0c	110	8	the	the	DT
cord-263987-ff6kor0c	110	9	extension	extension	NN
cord-263987-ff6kor0c	110	10	from	from	IN
cord-263987-ff6kor0c	110	11	pairwise	pairwise	JJ
cord-263987-ff6kor0c	110	12	probability	probability	NN
cord-263987-ff6kor0c	110	13	distributions	distribution	NNS
cord-263987-ff6kor0c	110	14	to	to	TO
cord-263987-ff6kor0c	110	15	phylogenetic	phylogenetic	VB
cord-263987-ff6kor0c	110	16	likelihoods	likelihood	NNS
cord-263987-ff6kor0c	110	17	of	of	IN
cord-263987-ff6kor0c	110	18	multiple	multiple	JJ
cord-263987-ff6kor0c	110	19	sequences	sequence	NNS
cord-263987-ff6kor0c	110	20	,	,	,
cord-263987-ff6kor0c	110	21	using	use	VBG
cord-263987-ff6kor0c	110	22	analogs	analog	NNS
cord-263987-ff6kor0c	110	23	of	of	IN
cord-263987-ff6kor0c	110	24	Felsenstein	Felsenstein	NNP
cord-263987-ff6kor0c	110	25	's	's	POS
cord-263987-ff6kor0c	110	26	pruning	pruning	NN
cord-263987-ff6kor0c	110	27	recursion	recursion	NN
cord-263987-ff6kor0c	110	28	(	(	-LRB-
cord-263987-ff6kor0c	110	29	Eq	Eq	NNP
cord-263987-ff6kor0c	110	30	.	.	NNP
cord-263987-ff6kor0c	110	31	4	4	CD
cord-263987-ff6kor0c	110	32	)	)	-RRB-
cord-263987-ff6kor0c	110	33	.	.	.
cord-263987-ff6kor0c	111	1	This	this	DT
cord-263987-ff6kor0c	111	2	section	section	NN
cord-263987-ff6kor0c	111	3	begins	begin	VBZ
cord-263987-ff6kor0c	111	4	with	with	IN
cord-263987-ff6kor0c	111	5	various	various	JJ
cord-263987-ff6kor0c	111	6	approaches	approach	NNS
cord-263987-ff6kor0c	111	7	to	to	IN
cord-263987-ff6kor0c	111	8	finding	find	VBG
cord-263987-ff6kor0c	111	9	the	the	DT
cord-263987-ff6kor0c	111	10	time	time	NN
cord-263987-ff6kor0c	111	11	-	-	HYPH
cord-263987-ff6kor0c	111	12	dependent	dependent	JJ
cord-263987-ff6kor0c	111	13	probability	probability	NN
cord-263987-ff6kor0c	111	14	distribution	distribution	NN
cord-263987-ff6kor0c	111	15	of	of	IN
cord-263987-ff6kor0c	111	16	gap	gap	NN
cord-263987-ff6kor0c	111	17	lengths	length	NNS
cord-263987-ff6kor0c	111	18	in	in	IN
cord-263987-ff6kor0c	111	19	a	a	DT
cord-263987-ff6kor0c	111	20	pairwise	pairwise	JJ
cord-263987-ff6kor0c	111	21	alignment	alignment	NN
cord-263987-ff6kor0c	111	22	,	,	,
cord-263987-ff6kor0c	111	23	under	under	IN
cord-263987-ff6kor0c	111	24	several	several	JJ
cord-263987-ff6kor0c	111	25	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	111	26	models	model	NNS
cord-263987-ff6kor0c	111	27	.	.	.
cord-263987-ff6kor0c	112	1	As	as	IN
cord-263987-ff6kor0c	112	2	an	an	DT
cord-263987-ff6kor0c	112	3	approach	approach	NN
cord-263987-ff6kor0c	112	4	to	to	IN
cord-263987-ff6kor0c	112	5	models	model	NNS
cord-263987-ff6kor0c	112	6	on	on	IN
cord-263987-ff6kor0c	112	7	strings	string	NNS
cord-263987-ff6kor0c	112	8	of	of	IN
cord-263987-ff6kor0c	112	9	unbounded	unbounded	JJ
cord-263987-ff6kor0c	112	10	length	length	NN
cord-263987-ff6kor0c	112	11	,	,	,
cord-263987-ff6kor0c	112	12	one	one	PRP
cord-263987-ff6kor0c	112	13	can	can	MD
cord-263987-ff6kor0c	112	14	consider	consider	VB
cord-263987-ff6kor0c	112	15	short	short	JJ
cord-263987-ff6kor0c	112	16	motifs	motif	NNS
cord-263987-ff6kor0c	112	17	of	of	IN
cord-263987-ff6kor0c	112	18	k	k	NN
cord-263987-ff6kor0c	112	19	residues	residue	NNS
cord-263987-ff6kor0c	112	20	.	.	.
cord-263987-ff6kor0c	113	1	These	these	DT
cord-263987-ff6kor0c	113	2	can	can	MD
cord-263987-ff6kor0c	113	3	still	still	RB
cord-263987-ff6kor0c	113	4	be	be	VB
cord-263987-ff6kor0c	113	5	considered	consider	VBN
cord-263987-ff6kor0c	113	6	as	as	IN
cord-263987-ff6kor0c	113	7	finite	finite	JJ
cord-263987-ff6kor0c	113	8	state	state	NN
cord-263987-ff6kor0c	113	9	-	-	HYPH
cord-263987-ff6kor0c	113	10	space	space	NN
cord-263987-ff6kor0c	113	11	models	model	NNS
cord-263987-ff6kor0c	113	12	;	;	:
cord-263987-ff6kor0c	113	13	for	for	IN
cord-263987-ff6kor0c	113	14	example	example	NN
cord-263987-ff6kor0c	113	15	,	,	,
cord-263987-ff6kor0c	113	16	a	a	DT
cord-263987-ff6kor0c	113	17	k	k	NN
cord-263987-ff6kor0c	113	18	-	-	HYPH
cord-263987-ff6kor0c	113	19	nucleotide	nucleotide	JJ
cord-263987-ff6kor0c	113	20	model	model	NN
cord-263987-ff6kor0c	113	21	has	have	VBZ
cord-263987-ff6kor0c	113	22	4	4	CD
cord-263987-ff6kor0c	113	23	k	k	NNP
cord-263987-ff6kor0c	113	24	possible	possible	JJ
cord-263987-ff6kor0c	113	25	states	state	NNS
cord-263987-ff6kor0c	113	26	.	.	.
cord-263987-ff6kor0c	114	1	Several	several	JJ
cord-263987-ff6kor0c	114	2	such	such	JJ
cord-263987-ff6kor0c	114	3	models	model	NNS
cord-263987-ff6kor0c	114	4	have	have	VBP
cord-263987-ff6kor0c	114	5	been	be	VBN
cord-263987-ff6kor0c	114	6	analyzed	analyze	VBN
cord-263987-ff6kor0c	114	7	,	,	,
cord-263987-ff6kor0c	114	8	including	include	VBG
cord-263987-ff6kor0c	114	9	models	model	NNS
cord-263987-ff6kor0c	114	10	on	on	IN
cord-263987-ff6kor0c	114	11	codons	codon	NNS
cord-263987-ff6kor0c	114	12	where	where	WRB
cord-263987-ff6kor0c	114	13	k	k	NN
cord-263987-ff6kor0c	114	14	=	=	SYM
cord-263987-ff6kor0c	114	15	3	3	CD
cord-263987-ff6kor0c	114	16	[	[	-LRB-
cord-263987-ff6kor0c	114	17	47	47	CD
cord-263987-ff6kor0c	114	18	,	,	,
cord-263987-ff6kor0c	114	19	58	58	CD
cord-263987-ff6kor0c	114	20	]	]	-RRB-
cord-263987-ff6kor0c	114	21	,	,	,
cord-263987-ff6kor0c	114	22	dinucleotides	dinucleotide	NNS
cord-263987-ff6kor0c	114	23	involved	involve	VBN
cord-263987-ff6kor0c	114	24	in	in	IN
cord-263987-ff6kor0c	114	25	RNA	RNA	NNP
cord-263987-ff6kor0c	114	26	basepairs	basepair	NNS
cord-263987-ff6kor0c	114	27	where	where	WRB
cord-263987-ff6kor0c	114	28	k	k	NN
cord-263987-ff6kor0c	114	29	=	=	SYM
cord-263987-ff6kor0c	114	30	2	2	CD
cord-263987-ff6kor0c	114	31	[	[	-LRB-
cord-263987-ff6kor0c	114	32	59	59	CD
cord-263987-ff6kor0c	114	33	]	]	-RRB-
cord-263987-ff6kor0c	114	34	[	[	-LRB-
cord-263987-ff6kor0c	114	35	60	60	CD
cord-263987-ff6kor0c	114	36	]	]	-RRB-
cord-263987-ff6kor0c	114	37	[	[	-LRB-
cord-263987-ff6kor0c	114	38	61	61	CD
cord-263987-ff6kor0c	114	39	]	]	-RRB-
cord-263987-ff6kor0c	114	40	,	,	,
cord-263987-ff6kor0c	114	41	and	and	CC
cord-263987-ff6kor0c	114	42	models	model	NNS
cord-263987-ff6kor0c	114	43	over	over	IN
cord-263987-ff6kor0c	114	44	sequences	sequence	NNS
cord-263987-ff6kor0c	114	45	of	of	IN
cord-263987-ff6kor0c	114	46	arbitrary	arbitrary	JJ
cord-263987-ff6kor0c	114	47	length	length	NN
cord-263987-ff6kor0c	115	1	k	k	NNP
cord-263987-ff6kor0c	115	2	[	[	-LRB-
cord-263987-ff6kor0c	115	3	44	44	CD
cord-263987-ff6kor0c	115	4	,	,	,
cord-263987-ff6kor0c	115	5	62	62	CD
cord-263987-ff6kor0c	115	6	]	]	-RRB-
cord-263987-ff6kor0c	115	7	.	.	.
cord-263987-ff6kor0c	116	1	Mostly	mostly	RB
cord-263987-ff6kor0c	116	2	,	,	,
cord-263987-ff6kor0c	116	3	these	these	DT
cord-263987-ff6kor0c	116	4	models	model	NNS
cord-263987-ff6kor0c	116	5	handle	handle	VBP
cord-263987-ff6kor0c	116	6	short	short	JJ
cord-263987-ff6kor0c	116	7	sequences	sequence	NNS
cord-263987-ff6kor0c	116	8	(	(	-LRB-
cord-263987-ff6kor0c	116	9	motifs	motif	NNS
cord-263987-ff6kor0c	116	10	)	)	-RRB-
cord-263987-ff6kor0c	116	11	and	and	CC
cord-263987-ff6kor0c	116	12	do	do	VBP
cord-263987-ff6kor0c	116	13	not	not	RB
cord-263987-ff6kor0c	116	14	allow	allow	VB
cord-263987-ff6kor0c	116	15	the	the	DT
cord-263987-ff6kor0c	116	16	sequence	sequence	NN
cord-263987-ff6kor0c	116	17	length	length	NN
cord-263987-ff6kor0c	116	18	to	to	TO
cord-263987-ff6kor0c	116	19	change	change	VB
cord-263987-ff6kor0c	116	20	over	over	IN
cord-263987-ff6kor0c	116	21	time	time	NN
cord-263987-ff6kor0c	116	22	(	(	-LRB-
cord-263987-ff6kor0c	116	23	so	so	RB
cord-263987-ff6kor0c	116	24	they	-PRON-	PRP
cord-263987-ff6kor0c	116	25	model	model	VBP
cord-263987-ff6kor0c	116	26	only	only	RB
cord-263987-ff6kor0c	116	27	substitutions	substitution	NNS
cord-263987-ff6kor0c	116	28	and	and	CC
cord-263987-ff6kor0c	116	29	not	not	RB
cord-263987-ff6kor0c	116	30	indels	indel	NNS
cord-263987-ff6kor0c	116	31	)	)	-RRB-
cord-263987-ff6kor0c	116	32	.	.	.
cord-263987-ff6kor0c	117	1	Some	some	DT
cord-263987-ff6kor0c	117	2	of	of	IN
cord-263987-ff6kor0c	117	3	the	the	DT
cord-263987-ff6kor0c	117	4	later	later	JJ
cord-263987-ff6kor0c	117	5	models	model	NNS
cord-263987-ff6kor0c	117	6	do	do	VBP
cord-263987-ff6kor0c	117	7	allow	allow	VB
cord-263987-ff6kor0c	117	8	the	the	DT
cord-263987-ff6kor0c	117	9	sequence	sequence	NN
cord-263987-ff6kor0c	117	10	length	length	NN
cord-263987-ff6kor0c	117	11	to	to	TO
cord-263987-ff6kor0c	117	12	change	change	VB
cord-263987-ff6kor0c	117	13	via	via	IN
cord-263987-ff6kor0c	117	14	insertions	insertion	NNS
cord-263987-ff6kor0c	117	15	or	or	CC
cord-263987-ff6kor0c	117	16	deletions	deletion	NNS
cord-263987-ff6kor0c	117	17	[	[	-LRB-
cord-263987-ff6kor0c	117	18	62	62	CD
cord-263987-ff6kor0c	117	19	]	]	-RRB-
cord-263987-ff6kor0c	117	20	though	though	IN
cord-263987-ff6kor0c	117	21	these	these	DT
cord-263987-ff6kor0c	117	22	models	model	NNS
cord-263987-ff6kor0c	117	23	have	have	VBP
cord-263987-ff6kor0c	117	24	not	not	RB
cord-263987-ff6kor0c	117	25	yet	yet	RB
cord-263987-ff6kor0c	117	26	been	be	VBN
cord-263987-ff6kor0c	117	27	analyzed	analyze	VBN
cord-263987-ff6kor0c	117	28	in	in	IN
cord-263987-ff6kor0c	117	29	a	a	DT
cord-263987-ff6kor0c	117	30	way	way	NN
cord-263987-ff6kor0c	117	31	that	that	WDT
cord-263987-ff6kor0c	117	32	would	would	MD
cord-263987-ff6kor0c	117	33	allow	allow	VB
cord-263987-ff6kor0c	117	34	the	the	DT
cord-263987-ff6kor0c	117	35	computation	computation	NN
cord-263987-ff6kor0c	117	36	of	of	IN
cord-263987-ff6kor0c	117	37	alignment	alignment	NN
cord-263987-ff6kor0c	117	38	likelihoods	likelihood	NNS
cord-263987-ff6kor0c	117	39	for	for	IN
cord-263987-ff6kor0c	117	40	sequences	sequence	NNS
cord-263987-ff6kor0c	117	41	of	of	IN
cord-263987-ff6kor0c	117	42	realistic	realistic	JJ
cord-263987-ff6kor0c	117	43	lengths	length	NNS
cord-263987-ff6kor0c	117	44	.	.	.
cord-263987-ff6kor0c	118	1	It	-PRON-	PRP
cord-263987-ff6kor0c	118	2	is	be	VBZ
cord-263987-ff6kor0c	118	3	a	a	DT
cord-263987-ff6kor0c	118	4	remarkable	remarkable	JJ
cord-263987-ff6kor0c	118	5	reflection	reflection	NN
cord-263987-ff6kor0c	118	6	on	on	IN
cord-263987-ff6kor0c	118	7	the	the	DT
cord-263987-ff6kor0c	118	8	extremely	extremely	RB
cord-263987-ff6kor0c	118	9	challenging	challenging	JJ
cord-263987-ff6kor0c	118	10	nature	nature	NN
cord-263987-ff6kor0c	118	11	of	of	IN
cord-263987-ff6kor0c	118	12	this	this	DT
cord-263987-ff6kor0c	118	13	problem	problem	NN
cord-263987-ff6kor0c	118	14	that	that	IN
cord-263987-ff6kor0c	118	15	,	,	,
cord-263987-ff6kor0c	118	16	to	to	IN
cord-263987-ff6kor0c	118	17	date	date	NN
cord-263987-ff6kor0c	118	18	,	,	,
cord-263987-ff6kor0c	118	19	the	the	DT
cord-263987-ff6kor0c	118	20	only	only	JJ
cord-263987-ff6kor0c	118	21	exactly	exactly	RB
cord-263987-ff6kor0c	118	22	solved	solve	VBD
cord-263987-ff6kor0c	118	23	indel	indel	NN
cord-263987-ff6kor0c	118	24	model	model	NN
cord-263987-ff6kor0c	118	25	on	on	IN
cord-263987-ff6kor0c	118	26	strings	string	NNS
cord-263987-ff6kor0c	118	27	is	be	VBZ
cord-263987-ff6kor0c	118	28	the	the	DT
cord-263987-ff6kor0c	118	29	TKF91	TKF91	NNP
cord-263987-ff6kor0c	118	30	model	model	NN
cord-263987-ff6kor0c	118	31	,	,	,
cord-263987-ff6kor0c	118	32	named	name	VBN
cord-263987-ff6kor0c	118	33	after	after	IN
cord-263987-ff6kor0c	118	34	the	the	DT
cord-263987-ff6kor0c	118	35	authors	author	NNS
cord-263987-ff6kor0c	118	36	'	'	POS
cord-263987-ff6kor0c	118	37	initials	initial	NNS
cord-263987-ff6kor0c	118	38	and	and	CC
cord-263987-ff6kor0c	118	39	date	date	NN
cord-263987-ff6kor0c	118	40	of	of	IN
cord-263987-ff6kor0c	118	41	publication	publication	NN
cord-263987-ff6kor0c	118	42	of	of	IN
cord-263987-ff6kor0c	118	43	this	this	DT
cord-263987-ff6kor0c	118	44	seminal	seminal	JJ
cord-263987-ff6kor0c	118	45	paper	paper	NN
cord-263987-ff6kor0c	118	46	[	[	-LRB-
cord-263987-ff6kor0c	118	47	63	63	CD
cord-263987-ff6kor0c	118	48	]	]	-RRB-
cord-263987-ff6kor0c	118	49	.	.	.
cord-263987-ff6kor0c	119	1	While	while	IN
cord-263987-ff6kor0c	119	2	there	there	EX
cord-263987-ff6kor0c	119	3	has	have	VBZ
cord-263987-ff6kor0c	119	4	been	be	VBN
cord-263987-ff6kor0c	119	5	progress	progress	NN
cord-263987-ff6kor0c	119	6	in	in	IN
cord-263987-ff6kor0c	119	7	developing	develop	VBG
cord-263987-ff6kor0c	119	8	approximate	approximate	JJ
cord-263987-ff6kor0c	119	9	models	model	NNS
cord-263987-ff6kor0c	119	10	in	in	IN
cord-263987-ff6kor0c	119	11	the	the	DT
cord-263987-ff6kor0c	119	12	25	25	CD
cord-263987-ff6kor0c	119	13	years	year	NNS
cord-263987-ff6kor0c	119	14	since	since	IN
cord-263987-ff6kor0c	119	15	the	the	DT
cord-263987-ff6kor0c	119	16	publication	publication	NN
cord-263987-ff6kor0c	119	17	of	of	IN
cord-263987-ff6kor0c	119	18	this	this	DT
cord-263987-ff6kor0c	119	19	paper	paper	NN
cord-263987-ff6kor0c	119	20	,	,	,
cord-263987-ff6kor0c	119	21	and	and	CC
cord-263987-ff6kor0c	119	22	in	in	IN
cord-263987-ff6kor0c	119	23	extending	extend	VBG
cord-263987-ff6kor0c	119	24	it	-PRON-	PRP
cord-263987-ff6kor0c	119	25	from	from	IN
cord-263987-ff6kor0c	119	26	pairwise	pairwise	JJ
cord-263987-ff6kor0c	119	27	to	to	IN
cord-263987-ff6kor0c	119	28	multiple	multiple	JJ
cord-263987-ff6kor0c	119	29	sequence	sequence	NN
cord-263987-ff6kor0c	119	30	alignment	alignment	NN
cord-263987-ff6kor0c	119	31	,	,	,
cord-263987-ff6kor0c	119	32	it	-PRON-	PRP
cord-263987-ff6kor0c	119	33	remains	remain	VBZ
cord-263987-ff6kor0c	119	34	the	the	DT
cord-263987-ff6kor0c	119	35	only	only	JJ
cord-263987-ff6kor0c	119	36	model	model	NN
cord-263987-ff6kor0c	119	37	for	for	IN
cord-263987-ff6kor0c	119	38	which	which	WDT
cord-263987-ff6kor0c	119	39	1	1	CD
cord-263987-ff6kor0c	119	40	.	.	.
cord-263987-ff6kor0c	120	1	the	the	DT
cord-263987-ff6kor0c	120	2	state	state	NN
cord-263987-ff6kor0c	120	3	space	space	NN
cord-263987-ff6kor0c	120	4	is	be	VBZ
cord-263987-ff6kor0c	120	5	the	the	DT
cord-263987-ff6kor0c	120	6	set	set	NN
cord-263987-ff6kor0c	120	7	of	of	IN
cord-263987-ff6kor0c	120	8	all	all	DT
cord-263987-ff6kor0c	120	9	sequences	sequence	NNS
cord-263987-ff6kor0c	120	10	(	(	-LRB-
cord-263987-ff6kor0c	120	11	strings	string	NNS
cord-263987-ff6kor0c	120	12	)	)	-RRB-
cord-263987-ff6kor0c	120	13	over	over	IN
cord-263987-ff6kor0c	120	14	a	a	DT
cord-263987-ff6kor0c	120	15	finite	finite	JJ
cord-263987-ff6kor0c	120	16	alphabet	alphabet	NN
cord-263987-ff6kor0c	120	17	,	,	,
cord-263987-ff6kor0c	120	18	2	2	CD
cord-263987-ff6kor0c	120	19	.	.	.
cord-263987-ff6kor0c	121	1	the	the	DT
cord-263987-ff6kor0c	121	2	state	state	NN
cord-263987-ff6kor0c	121	3	space	space	NN
cord-263987-ff6kor0c	121	4	is	be	VBZ
cord-263987-ff6kor0c	121	5	ergodically	ergodically	RB
cord-263987-ff6kor0c	121	6	explored	explore	VBN
cord-263987-ff6kor0c	121	7	by	by	IN
cord-263987-ff6kor0c	121	8	substitutions	substitution	NNS
cord-263987-ff6kor0c	121	9	and	and	CC
cord-263987-ff6kor0c	121	10	indels	indel	NNS
cord-263987-ff6kor0c	121	11	(	(	-LRB-
cord-263987-ff6kor0c	121	12	so	so	RB
cord-263987-ff6kor0c	121	13	there	there	EX
cord-263987-ff6kor0c	121	14	is	be	VBZ
cord-263987-ff6kor0c	121	15	a	a	DT
cord-263987-ff6kor0c	121	16	valid	valid	JJ
cord-263987-ff6kor0c	121	17	alignment	alignment	NN
cord-263987-ff6kor0c	121	18	and	and	CC
cord-263987-ff6kor0c	121	19	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	121	20	trajectory	trajectory	NN
cord-263987-ff6kor0c	121	21	between	between	IN
cord-263987-ff6kor0c	121	22	any	any	DT
cord-263987-ff6kor0c	121	23	two	two	CD
cord-263987-ff6kor0c	121	24	sequences	sequence	NNS
cord-263987-ff6kor0c	121	25	φ(0	φ(0	NFP
cord-263987-ff6kor0c	121	26	)	)	-RRB-
cord-263987-ff6kor0c	121	27	and	and	CC
cord-263987-ff6kor0c	121	28	φ(t	φ(t	NNP
cord-263987-ff6kor0c	121	29	)	)	-RRB-
cord-263987-ff6kor0c	121	30	)	)	-RRB-
cord-263987-ff6kor0c	121	31	,	,	,
cord-263987-ff6kor0c	121	32	3	3	CD
cord-263987-ff6kor0c	121	33	.	.	.
cord-263987-ff6kor0c	122	1	Equation	equation	NN
cord-263987-ff6kor0c	122	2	2	2	CD
cord-263987-ff6kor0c	122	3	can	can	MD
cord-263987-ff6kor0c	122	4	be	be	VB
cord-263987-ff6kor0c	122	5	calculated	calculate	VBN
cord-263987-ff6kor0c	122	6	exactly	exactly	RB
cord-263987-ff6kor0c	122	7	(	(	-LRB-
cord-263987-ff6kor0c	122	8	specifically	specifically	RB
cord-263987-ff6kor0c	122	9	,	,	,
cord-263987-ff6kor0c	122	10	as	as	IN
cord-263987-ff6kor0c	122	11	a	a	DT
cord-263987-ff6kor0c	122	12	sum	sum	NN
cord-263987-ff6kor0c	122	13	over	over	IN
cord-263987-ff6kor0c	122	14	alignments	alignment	NNS
cord-263987-ff6kor0c	122	15	,	,	,
cord-263987-ff6kor0c	122	16	where	where	WRB
cord-263987-ff6kor0c	122	17	the	the	DT
cord-263987-ff6kor0c	122	18	individual	individual	JJ
cord-263987-ff6kor0c	122	19	alignment	alignment	NN
cord-263987-ff6kor0c	122	20	likelihoods	likelihood	NNS
cord-263987-ff6kor0c	122	21	can	can	MD
cord-263987-ff6kor0c	122	22	be	be	VB
cord-263987-ff6kor0c	122	23	written	write	VBN
cord-263987-ff6kor0c	122	24	in	in	IN
cord-263987-ff6kor0c	122	25	closed	closed	JJ
cord-263987-ff6kor0c	122	26	form	form	NN
cord-263987-ff6kor0c	122	27	)	)	-RRB-
cord-263987-ff6kor0c	122	28	.	.	.
cord-263987-ff6kor0c	123	1	The	the	DT
cord-263987-ff6kor0c	123	2	TKF91	TKF91	NNP
cord-263987-ff6kor0c	123	3	model	model	NN
cord-263987-ff6kor0c	123	4	allows	allow	VBZ
cord-263987-ff6kor0c	123	5	single	single	JJ
cord-263987-ff6kor0c	123	6	-	-	HYPH
cord-263987-ff6kor0c	123	7	residue	residue	NN
cord-263987-ff6kor0c	123	8	contextindependent	contextindependent	NN
cord-263987-ff6kor0c	123	9	events	event	NNS
cord-263987-ff6kor0c	123	10	only	only	RB
cord-263987-ff6kor0c	123	11	.	.	.
cord-263987-ff6kor0c	124	1	These	these	DT
cord-263987-ff6kor0c	124	2	include	include	VBP
cord-263987-ff6kor0c	124	3	(	(	-LRB-
cord-263987-ff6kor0c	124	4	i	i	NN
cord-263987-ff6kor0c	124	5	)	)	-RRB-
cord-263987-ff6kor0c	124	6	single	single	JJ
cord-263987-ff6kor0c	124	7	-	-	HYPH
cord-263987-ff6kor0c	124	8	residue	residue	NN
cord-263987-ff6kor0c	124	9	substitutions	substitution	NNS
cord-263987-ff6kor0c	124	10	,	,	,
cord-263987-ff6kor0c	124	11	(	(	-LRB-
cord-263987-ff6kor0c	124	12	ii	ii	NN
cord-263987-ff6kor0c	124	13	)	)	-RRB-
cord-263987-ff6kor0c	124	14	single	single	JJ
cord-263987-ff6kor0c	124	15	-	-	HYPH
cord-263987-ff6kor0c	124	16	residue	residue	NN
cord-263987-ff6kor0c	124	17	insertions	insertion	NNS
cord-263987-ff6kor0c	124	18	(	(	-LRB-
cord-263987-ff6kor0c	124	19	with	with	IN
cord-263987-ff6kor0c	124	20	the	the	DT
cord-263987-ff6kor0c	124	21	inserted	insert	VBN
cord-263987-ff6kor0c	124	22	residue	residue	NN
cord-263987-ff6kor0c	124	23	drawn	draw	VBN
cord-263987-ff6kor0c	124	24	from	from	IN
cord-263987-ff6kor0c	124	25	the	the	DT
cord-263987-ff6kor0c	124	26	equilibrium	equilibrium	NN
cord-263987-ff6kor0c	124	27	distribution	distribution	NN
cord-263987-ff6kor0c	124	28	of	of	IN
cord-263987-ff6kor0c	124	29	the	the	DT
cord-263987-ff6kor0c	124	30	substitution	substitution	NN
cord-263987-ff6kor0c	124	31	process	process	NN
cord-263987-ff6kor0c	124	32	)	)	-RRB-
cord-263987-ff6kor0c	124	33	,	,	,
cord-263987-ff6kor0c	124	34	and	and	CC
cord-263987-ff6kor0c	124	35	(	(	-LRB-
cord-263987-ff6kor0c	124	36	iii	iii	NN
cord-263987-ff6kor0c	124	37	)	)	-RRB-
cord-263987-ff6kor0c	124	38	single	single	JJ
cord-263987-ff6kor0c	124	39	-	-	HYPH
cord-263987-ff6kor0c	124	40	residue	residue	NN
cord-263987-ff6kor0c	124	41	deletions	deletion	NNS
cord-263987-ff6kor0c	124	42	(	(	-LRB-
cord-263987-ff6kor0c	124	43	whose	whose	WP$
cord-263987-ff6kor0c	124	44	rates	rate	NNS
cord-263987-ff6kor0c	124	45	are	be	VBP
cord-263987-ff6kor0c	124	46	independent	independent	JJ
cord-263987-ff6kor0c	124	47	of	of	IN
cord-263987-ff6kor0c	124	48	the	the	DT
cord-263987-ff6kor0c	124	49	residue	residue	NN
cord-263987-ff6kor0c	124	50	being	be	VBG
cord-263987-ff6kor0c	124	51	deleted	delete	VBN
cord-263987-ff6kor0c	124	52	)	)	-RRB-
cord-263987-ff6kor0c	124	53	.	.	.
cord-263987-ff6kor0c	125	1	The	the	DT
cord-263987-ff6kor0c	125	2	rates	rate	NNS
cord-263987-ff6kor0c	125	3	of	of	IN
cord-263987-ff6kor0c	125	4	all	all	PDT
cord-263987-ff6kor0c	125	5	these	these	DT
cord-263987-ff6kor0c	125	6	mutation	mutation	NN
cord-263987-ff6kor0c	125	7	events	event	NNS
cord-263987-ff6kor0c	125	8	are	be	VBP
cord-263987-ff6kor0c	125	9	independent	independent	JJ
cord-263987-ff6kor0c	125	10	of	of	IN
cord-263987-ff6kor0c	125	11	the	the	DT
cord-263987-ff6kor0c	125	12	flanking	flanking	JJ
cord-263987-ff6kor0c	125	13	sequence	sequence	NN
cord-263987-ff6kor0c	125	14	.	.	.
cord-263987-ff6kor0c	126	1	This	this	DT
cord-263987-ff6kor0c	126	2	process	process	NN
cord-263987-ff6kor0c	126	3	is	be	VBZ
cord-263987-ff6kor0c	126	4	equivalent	equivalent	JJ
cord-263987-ff6kor0c	126	5	to	to	IN
cord-263987-ff6kor0c	126	6	a	a	DT
cord-263987-ff6kor0c	126	7	linear	linear	JJ
cord-263987-ff6kor0c	126	8	birth	birth	NN
cord-263987-ff6kor0c	126	9	-	-	HYPH
cord-263987-ff6kor0c	126	10	death	death	NN
cord-263987-ff6kor0c	126	11	model	model	NN
cord-263987-ff6kor0c	126	12	with	with	IN
cord-263987-ff6kor0c	126	13	constant	constant	JJ
cord-263987-ff6kor0c	126	14	immigration	immigration	NN
cord-263987-ff6kor0c	126	15	[	[	-LRB-
cord-263987-ff6kor0c	126	16	64	64	CD
cord-263987-ff6kor0c	126	17	]	]	-RRB-
cord-263987-ff6kor0c	126	18	.	.	.
cord-263987-ff6kor0c	127	1	Thorne	Thorne	NNP
cord-263987-ff6kor0c	127	2	et	et	NNP
cord-263987-ff6kor0c	127	3	al	al	NNP
cord-263987-ff6kor0c	127	4	.	.	NNP
cord-263987-ff6kor0c	127	5	showed	show	VBD
cord-263987-ff6kor0c	127	6	that	that	IN
cord-263987-ff6kor0c	127	7	an	an	DT
cord-263987-ff6kor0c	127	8	ancestral	ancestral	JJ
cord-263987-ff6kor0c	127	9	sequence	sequence	NN
cord-263987-ff6kor0c	127	10	can	can	MD
cord-263987-ff6kor0c	127	11	be	be	VB
cord-263987-ff6kor0c	127	12	split	split	VBN
cord-263987-ff6kor0c	127	13	into	into	IN
cord-263987-ff6kor0c	127	14	independently	independently	RB
cord-263987-ff6kor0c	127	15	evolving	evolve	VBG
cord-263987-ff6kor0c	127	16	zones	zone	NNS
cord-263987-ff6kor0c	127	17	,	,	,
cord-263987-ff6kor0c	127	18	one	one	CD
cord-263987-ff6kor0c	127	19	for	for	IN
cord-263987-ff6kor0c	127	20	each	each	DT
cord-263987-ff6kor0c	127	21	ancestral	ancestral	JJ
cord-263987-ff6kor0c	127	22	residue	residue	NN
cord-263987-ff6kor0c	127	23	(	(	-LRB-
cord-263987-ff6kor0c	127	24	or	or	CC
cord-263987-ff6kor0c	127	25	"	"	``
cord-263987-ff6kor0c	127	26	links	link	NNS
cord-263987-ff6kor0c	127	27	"	"	''
cord-263987-ff6kor0c	127	28	,	,	,
cord-263987-ff6kor0c	127	29	as	as	IN
cord-263987-ff6kor0c	127	30	they	-PRON-	PRP
cord-263987-ff6kor0c	127	31	call	call	VBP
cord-263987-ff6kor0c	127	32	them	-PRON-	PRP
cord-263987-ff6kor0c	127	33	)	)	-RRB-
cord-263987-ff6kor0c	127	34	.	.	.
cord-263987-ff6kor0c	128	1	This	this	DT
cord-263987-ff6kor0c	128	2	leads	lead	VBZ
cord-263987-ff6kor0c	128	3	to	to	IN
cord-263987-ff6kor0c	128	4	the	the	DT
cord-263987-ff6kor0c	128	5	very	very	RB
cord-263987-ff6kor0c	128	6	appealing	appealing	JJ
cord-263987-ff6kor0c	128	7	result	result	NN
cord-263987-ff6kor0c	128	8	that	that	IN
cord-263987-ff6kor0c	128	9	the	the	DT
cord-263987-ff6kor0c	128	10	length	length	NN
cord-263987-ff6kor0c	128	11	distribution	distribution	NN
cord-263987-ff6kor0c	128	12	for	for	IN
cord-263987-ff6kor0c	128	13	observed	observed	JJ
cord-263987-ff6kor0c	128	14	gaps	gap	NNS
cord-263987-ff6kor0c	128	15	is	be	VBZ
cord-263987-ff6kor0c	128	16	geometric	geometric	JJ
cord-263987-ff6kor0c	128	17	,	,	,
cord-263987-ff6kor0c	128	18	which	which	WDT
cord-263987-ff6kor0c	128	19	conveniently	conveniently	RB
cord-263987-ff6kor0c	128	20	allows	allow	VBZ
cord-263987-ff6kor0c	128	21	the	the	DT
cord-263987-ff6kor0c	128	22	joint	joint	JJ
cord-263987-ff6kor0c	128	23	probability	probability	NN
cord-263987-ff6kor0c	128	24	P(φ(0	P(φ(0	NNPS
cord-263987-ff6kor0c	128	25	)	)	-RRB-
cord-263987-ff6kor0c	128	26	,	,	,
cord-263987-ff6kor0c	128	27	φ(t	φ(t	NNP
cord-263987-ff6kor0c	128	28	)	)	-RRB-
cord-263987-ff6kor0c	128	29	)	)	-RRB-
cord-263987-ff6kor0c	128	30	to	to	TO
cord-263987-ff6kor0c	128	31	be	be	VB
cord-263987-ff6kor0c	128	32	expressed	express	VBN
cord-263987-ff6kor0c	128	33	as	as	IN
cord-263987-ff6kor0c	128	34	a	a	DT
cord-263987-ff6kor0c	128	35	paired	pair	VBN
cord-263987-ff6kor0c	128	36	-	-	HYPH
cord-263987-ff6kor0c	128	37	sequence	sequence	NN
cord-263987-ff6kor0c	128	38	Hidden	Hidden	NNP
cord-263987-ff6kor0c	128	39	Markov	Markov	NNP
cord-263987-ff6kor0c	128	40	Model	Model	NNP
cord-263987-ff6kor0c	128	41	or	or	CC
cord-263987-ff6kor0c	128	42	"	"	``
cord-263987-ff6kor0c	128	43	Pair	pair	VB
cord-263987-ff6kor0c	128	44	HMM	hmm	NN
cord-263987-ff6kor0c	128	45	"	"	''
cord-263987-ff6kor0c	128	46	[	[	-LRB-
cord-263987-ff6kor0c	128	47	65	65	CD
cord-263987-ff6kor0c	128	48	]	]	-RRB-
cord-263987-ff6kor0c	128	49	.	.	.
cord-263987-ff6kor0c	129	1	The	the	DT
cord-263987-ff6kor0c	129	2	conditional	conditional	JJ
cord-263987-ff6kor0c	129	3	probability	probability	NN
cord-263987-ff6kor0c	129	4	P(φ(t)|φ(0	P(φ(t)|φ(0	NNP
cord-263987-ff6kor0c	129	5	)	)	-RRB-
cord-263987-ff6kor0c	129	6	)	)	-RRB-
cord-263987-ff6kor0c	129	7	can	can	MD
cord-263987-ff6kor0c	129	8	similarly	similarly	RB
cord-263987-ff6kor0c	129	9	be	be	VB
cord-263987-ff6kor0c	129	10	expressed	express	VBN
cord-263987-ff6kor0c	129	11	as	as	IN
cord-263987-ff6kor0c	129	12	a	a	DT
cord-263987-ff6kor0c	129	13	weighted	weighted	JJ
cord-263987-ff6kor0c	129	14	finite	finite	JJ
cord-263987-ff6kor0c	129	15	-	-	HYPH
cord-263987-ff6kor0c	129	16	state	state	NN
cord-263987-ff6kor0c	129	17	transducer	transducer	NN
cord-263987-ff6kor0c	129	18	[	[	-LRB-
cord-263987-ff6kor0c	129	19	66	66	CD
cord-263987-ff6kor0c	129	20	]	]	-RRB-
cord-263987-ff6kor0c	129	21	[	[	-LRB-
cord-263987-ff6kor0c	129	22	67	67	CD
cord-263987-ff6kor0c	129	23	]	]	-RRB-
cord-263987-ff6kor0c	129	24	[	[	-LRB-
cord-263987-ff6kor0c	129	25	68	68	CD
cord-263987-ff6kor0c	129	26	]	]	-RRB-
cord-263987-ff6kor0c	129	27	.	.	.
cord-263987-ff6kor0c	130	1	Some	some	DT
cord-263987-ff6kor0c	130	2	interesting	interesting	JJ
cord-263987-ff6kor0c	130	3	discussion	discussion	NN
cord-263987-ff6kor0c	130	4	of	of	IN
cord-263987-ff6kor0c	130	5	why	why	WRB
cord-263987-ff6kor0c	130	6	the	the	DT
cord-263987-ff6kor0c	130	7	TKF91	TKF91	NNP
cord-263987-ff6kor0c	130	8	model	model	NN
cord-263987-ff6kor0c	130	9	should	should	MD
cord-263987-ff6kor0c	130	10	be	be	VB
cord-263987-ff6kor0c	130	11	solvable	solvable	JJ
cord-263987-ff6kor0c	130	12	at	at	RB
cord-263987-ff6kor0c	130	13	all	all	DT
cord-263987-ff6kor0c	130	14	can	can	MD
cord-263987-ff6kor0c	130	15	be	be	VB
cord-263987-ff6kor0c	130	16	found	find	VBN
cord-263987-ff6kor0c	130	17	in	in	IN
cord-263987-ff6kor0c	130	18	[	[	-LRB-
cord-263987-ff6kor0c	130	19	69	69	CD
cord-263987-ff6kor0c	130	20	]	]	-RRB-
cord-263987-ff6kor0c	130	21	and	and	CC
cord-263987-ff6kor0c	130	22	in	in	IN
cord-263987-ff6kor0c	130	23	[	[	-LRB-
cord-263987-ff6kor0c	130	24	42	42	CD
cord-263987-ff6kor0c	130	25	]	]	-RRB-
cord-263987-ff6kor0c	130	26	.	.	.
cord-263987-ff6kor0c	131	1	There	there	EX
cord-263987-ff6kor0c	131	2	are	be	VBP
cord-263987-ff6kor0c	131	3	several	several	JJ
cord-263987-ff6kor0c	131	4	variations	variation	NNS
cord-263987-ff6kor0c	131	5	on	on	IN
cord-263987-ff6kor0c	131	6	the	the	DT
cord-263987-ff6kor0c	131	7	TKF91	TKF91	NNP
cord-263987-ff6kor0c	131	8	model	model	NN
cord-263987-ff6kor0c	131	9	.	.	.
cord-263987-ff6kor0c	132	1	The	the	DT
cord-263987-ff6kor0c	132	2	case	case	NN
cord-263987-ff6kor0c	132	3	where	where	WRB
cord-263987-ff6kor0c	132	4	there	there	EX
cord-263987-ff6kor0c	132	5	are	be	VBP
cord-263987-ff6kor0c	132	6	no	no	DT
cord-263987-ff6kor0c	132	7	indels	indel	NNS
cord-263987-ff6kor0c	132	8	at	at	RB
cord-263987-ff6kor0c	132	9	all	all	RB
cord-263987-ff6kor0c	132	10	,	,	,
cord-263987-ff6kor0c	132	11	only	only	RB
cord-263987-ff6kor0c	132	12	substitutions	substitution	NNS
cord-263987-ff6kor0c	132	13	,	,	,
cord-263987-ff6kor0c	132	14	can	can	MD
cord-263987-ff6kor0c	132	15	be	be	VB
cord-263987-ff6kor0c	132	16	viewed	view	VBN
cord-263987-ff6kor0c	132	17	as	as	IN
cord-263987-ff6kor0c	132	18	a	a	DT
cord-263987-ff6kor0c	132	19	special	special	JJ
cord-263987-ff6kor0c	132	20	case	case	NN
cord-263987-ff6kor0c	132	21	of	of	IN
cord-263987-ff6kor0c	132	22	TKF91	TKF91	NNP
cord-263987-ff6kor0c	132	23	,	,	,
cord-263987-ff6kor0c	132	24	and	and	CC
cord-263987-ff6kor0c	132	25	can	can	MD
cord-263987-ff6kor0c	132	26	of	of	IN
cord-263987-ff6kor0c	132	27	course	course	NN
cord-263987-ff6kor0c	132	28	be	be	VB
cord-263987-ff6kor0c	132	29	solved	solve	VBN
cord-263987-ff6kor0c	132	30	exactly	exactly	RB
cord-263987-ff6kor0c	132	31	,	,	,
cord-263987-ff6kor0c	132	32	as	as	IN
cord-263987-ff6kor0c	132	33	is	be	VBZ
cord-263987-ff6kor0c	132	34	well	well	RB
cord-263987-ff6kor0c	132	35	known	known	JJ
cord-263987-ff6kor0c	132	36	.	.	.
cord-263987-ff6kor0c	133	1	Another	another	DT
cord-263987-ff6kor0c	133	2	variation	variation	NN
cord-263987-ff6kor0c	133	3	on	on	IN
cord-263987-ff6kor0c	133	4	the	the	DT
cord-263987-ff6kor0c	133	5	TKF91	TKF91	NNP
cord-263987-ff6kor0c	133	6	model	model	NN
cord-263987-ff6kor0c	133	7	constrains	constrain	VBZ
cord-263987-ff6kor0c	133	8	the	the	DT
cord-263987-ff6kor0c	133	9	total	total	JJ
cord-263987-ff6kor0c	133	10	indel	indel	NN
cord-263987-ff6kor0c	133	11	rate	rate	NN
cord-263987-ff6kor0c	133	12	to	to	TO
cord-263987-ff6kor0c	133	13	be	be	VB
cord-263987-ff6kor0c	133	14	independent	independent	JJ
cord-263987-ff6kor0c	133	15	of	of	IN
cord-263987-ff6kor0c	133	16	sequence	sequence	NN
cord-263987-ff6kor0c	133	17	length	length	NN
cord-263987-ff6kor0c	133	18	[	[	-LRB-
cord-263987-ff6kor0c	133	19	70	70	CD
cord-263987-ff6kor0c	133	20	]	]	-RRB-
cord-263987-ff6kor0c	133	21	.	.	.
cord-263987-ff6kor0c	134	1	In	in	IN
cord-263987-ff6kor0c	134	2	the	the	DT
cord-263987-ff6kor0c	134	3	following	following	JJ
cord-263987-ff6kor0c	134	4	section	section	NN
cord-263987-ff6kor0c	134	5	I	-PRON-	PRP
cord-263987-ff6kor0c	134	6	cover	cover	VBP
cord-263987-ff6kor0c	134	7	some	some	DT
cord-263987-ff6kor0c	134	8	variants	variant	NNS
cord-263987-ff6kor0c	134	9	that	that	WDT
cord-263987-ff6kor0c	134	10	use	use	VBP
cord-263987-ff6kor0c	134	11	different	different	JJ
cord-263987-ff6kor0c	134	12	state	state	NN
cord-263987-ff6kor0c	134	13	spaces	space	NNS
cord-263987-ff6kor0c	134	14	.	.	.
cord-263987-ff6kor0c	135	1	It	-PRON-	PRP
cord-263987-ff6kor0c	135	2	is	be	VBZ
cord-263987-ff6kor0c	135	3	difficult	difficult	JJ
cord-263987-ff6kor0c	135	4	to	to	TO
cord-263987-ff6kor0c	135	5	extend	extend	VB
cord-263987-ff6kor0c	135	6	TKF91	TKF91	NNP
cord-263987-ff6kor0c	135	7	to	to	IN
cord-263987-ff6kor0c	135	8	more	more	RBR
cord-263987-ff6kor0c	135	9	realistic	realistic	JJ
cord-263987-ff6kor0c	135	10	models	model	NNS
cord-263987-ff6kor0c	135	11	wherein	wherein	WRB
cord-263987-ff6kor0c	135	12	indels	indel	NNS
cord-263987-ff6kor0c	135	13	(	(	-LRB-
cord-263987-ff6kor0c	135	14	or	or	CC
cord-263987-ff6kor0c	135	15	substitutions	substitution	NNS
cord-263987-ff6kor0c	135	16	)	)	-RRB-
cord-263987-ff6kor0c	135	17	can	can	MD
cord-263987-ff6kor0c	135	18	affect	affect	VB
cord-263987-ff6kor0c	135	19	multiple	multiple	JJ
cord-263987-ff6kor0c	135	20	residues	residue	NNS
cord-263987-ff6kor0c	135	21	at	at	IN
cord-263987-ff6kor0c	135	22	once	once	RB
cord-263987-ff6kor0c	135	23	.	.	.
cord-263987-ff6kor0c	136	1	In	in	IN
cord-263987-ff6kor0c	136	2	such	such	JJ
cord-263987-ff6kor0c	136	3	models	model	NNS
cord-263987-ff6kor0c	136	4	,	,	,
cord-263987-ff6kor0c	136	5	the	the	DT
cord-263987-ff6kor0c	136	6	fate	fate	NN
cord-263987-ff6kor0c	136	7	of	of	IN
cord-263987-ff6kor0c	136	8	adjacent	adjacent	JJ
cord-263987-ff6kor0c	136	9	residues	residue	NNS
cord-263987-ff6kor0c	136	10	is	be	VBZ
cord-263987-ff6kor0c	136	11	no	no	DT
cord-263987-ff6kor0c	136	12	longer	long	RBR
cord-263987-ff6kor0c	136	13	independent	independent	JJ
cord-263987-ff6kor0c	136	14	,	,	,
cord-263987-ff6kor0c	136	15	since	since	IN
cord-263987-ff6kor0c	136	16	a	a	DT
cord-263987-ff6kor0c	136	17	single	single	JJ
cord-263987-ff6kor0c	136	18	event	event	NN
cord-263987-ff6kor0c	136	19	can	can	MD
cord-263987-ff6kor0c	136	20	span	span	VB
cord-263987-ff6kor0c	136	21	multiple	multiple	JJ
cord-263987-ff6kor0c	136	22	sites	site	NNS
cord-263987-ff6kor0c	136	23	.	.	.
cord-263987-ff6kor0c	137	1	As	as	IN
cord-263987-ff6kor0c	137	2	a	a	DT
cord-263987-ff6kor0c	137	3	way	way	NN
cord-263987-ff6kor0c	137	4	around	around	IN
cord-263987-ff6kor0c	137	5	this	this	DT
cord-263987-ff6kor0c	137	6	difficulty	difficulty	NN
cord-263987-ff6kor0c	137	7	,	,	,
cord-263987-ff6kor0c	137	8	several	several	JJ
cord-263987-ff6kor0c	137	9	researchers	researcher	NNS
cord-263987-ff6kor0c	137	10	have	have	VBP
cord-263987-ff6kor0c	137	11	developed	develop	VBN
cord-263987-ff6kor0c	137	12	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	137	13	models	model	NNS
cord-263987-ff6kor0c	137	14	where	where	WRB
cord-263987-ff6kor0c	137	15	the	the	DT
cord-263987-ff6kor0c	137	16	state	state	NN
cord-263987-ff6kor0c	137	17	is	be	VBZ
cord-263987-ff6kor0c	137	18	not	not	RB
cord-263987-ff6kor0c	137	19	a	a	DT
cord-263987-ff6kor0c	137	20	pure	pure	JJ
cord-263987-ff6kor0c	137	21	DNA	dna	NN
cord-263987-ff6kor0c	137	22	or	or	CC
cord-263987-ff6kor0c	137	23	protein	protein	NN
cord-263987-ff6kor0c	137	24	sequence	sequence	NN
cord-263987-ff6kor0c	137	25	,	,	,
cord-263987-ff6kor0c	137	26	but	but	CC
cord-263987-ff6kor0c	137	27	includes	include	VBZ
cord-263987-ff6kor0c	137	28	some	some	DT
cord-263987-ff6kor0c	137	29	extra	extra	JJ
cord-263987-ff6kor0c	137	30	"	"	``
cord-263987-ff6kor0c	137	31	hidden	hidden	JJ
cord-263987-ff6kor0c	137	32	"	"	''
cord-263987-ff6kor0c	137	33	information	information	NN
cord-263987-ff6kor0c	137	34	,	,	,
cord-263987-ff6kor0c	137	35	such	such	JJ
cord-263987-ff6kor0c	137	36	as	as	IN
cord-263987-ff6kor0c	137	37	boundaries	boundary	NNS
cord-263987-ff6kor0c	137	38	,	,	,
cord-263987-ff6kor0c	137	39	markers	marker	NNS
cord-263987-ff6kor0c	137	40	or	or	CC
cord-263987-ff6kor0c	137	41	other	other	JJ
cord-263987-ff6kor0c	137	42	latent	latent	JJ
cord-263987-ff6kor0c	137	43	structure	structure	NN
cord-263987-ff6kor0c	137	44	.	.	.
cord-263987-ff6kor0c	138	1	In	in	IN
cord-263987-ff6kor0c	138	2	some	some	DT
cord-263987-ff6kor0c	138	3	of	of	IN
cord-263987-ff6kor0c	138	4	these	these	DT
cord-263987-ff6kor0c	138	5	models	model	NNS
cord-263987-ff6kor0c	138	6	the	the	DT
cord-263987-ff6kor0c	138	7	sequence	sequence	NN
cord-263987-ff6kor0c	138	8	of	of	IN
cord-263987-ff6kor0c	138	9	residues	residue	NNS
cord-263987-ff6kor0c	138	10	is	be	VBZ
cord-263987-ff6kor0c	138	11	replaced	replace	VBN
cord-263987-ff6kor0c	138	12	by	by	IN
cord-263987-ff6kor0c	138	13	a	a	DT
cord-263987-ff6kor0c	138	14	sequence	sequence	NN
cord-263987-ff6kor0c	138	15	of	of	IN
cord-263987-ff6kor0c	138	16	indivisible	indivisible	JJ
cord-263987-ff6kor0c	138	17	fragments	fragment	NNS
cord-263987-ff6kor0c	138	18	,	,	,
cord-263987-ff6kor0c	138	19	each	each	DT
cord-263987-ff6kor0c	138	20	of	of	IN
cord-263987-ff6kor0c	138	21	which	which	WDT
cord-263987-ff6kor0c	138	22	can	can	MD
cord-263987-ff6kor0c	138	23	contain	contain	VB
cord-263987-ff6kor0c	138	24	more	more	JJR
cord-263987-ff6kor0c	138	25	than	than	IN
cord-263987-ff6kor0c	138	26	one	one	CD
cord-263987-ff6kor0c	138	27	residue	residue	NN
cord-263987-ff6kor0c	138	28	[	[	-LRB-
cord-263987-ff6kor0c	138	29	56	56	CD
cord-263987-ff6kor0c	138	30	,	,	,
cord-263987-ff6kor0c	138	31	69	69	CD
cord-263987-ff6kor0c	138	32	,	,	,
cord-263987-ff6kor0c	138	33	71	71	CD
cord-263987-ff6kor0c	138	34	]	]	-RRB-
cord-263987-ff6kor0c	138	35	.	.	.
cord-263987-ff6kor0c	139	1	These	these	DT
cord-263987-ff6kor0c	139	2	includes	include	VBZ
cord-263987-ff6kor0c	139	3	the	the	DT
cord-263987-ff6kor0c	139	4	TKF92	tkf92	JJ
cord-263987-ff6kor0c	139	5	model	model	NN
cord-263987-ff6kor0c	139	6	[	[	-LRB-
cord-263987-ff6kor0c	139	7	71	71	CD
cord-263987-ff6kor0c	139	8	]	]	-RRB-
cord-263987-ff6kor0c	139	9	which	which	WDT
cord-263987-ff6kor0c	139	10	is	be	VBZ
cord-263987-ff6kor0c	139	11	,	,	,
cord-263987-ff6kor0c	139	12	essentially	essentially	RB
cord-263987-ff6kor0c	139	13	,	,	,
cord-263987-ff6kor0c	139	14	TKF91	TKF91	NNP
cord-263987-ff6kor0c	139	15	with	with	IN
cord-263987-ff6kor0c	139	16	residues	residue	NNS
cord-263987-ff6kor0c	139	17	replaced	replace	VBN
cord-263987-ff6kor0c	139	18	by	by	IN
cord-263987-ff6kor0c	139	19	fragments	fragment	NNS
cord-263987-ff6kor0c	139	20	(	(	-LRB-
cord-263987-ff6kor0c	139	21	so	so	IN
cord-263987-ff6kor0c	139	22	the	the	DT
cord-263987-ff6kor0c	139	23	alphabet	alphabet	NN
cord-263987-ff6kor0c	139	24	itself	-PRON-	PRP
cord-263987-ff6kor0c	139	25	is	be	VBZ
cord-263987-ff6kor0c	139	26	the	the	DT
cord-263987-ff6kor0c	139	27	countably	countably	RB
cord-263987-ff6kor0c	139	28	infinite	infinite	JJ
cord-263987-ff6kor0c	139	29	set	set	NN
cord-263987-ff6kor0c	139	30	of	of	IN
cord-263987-ff6kor0c	139	31	all	all	DT
cord-263987-ff6kor0c	139	32	sequences	sequence	NNS
cord-263987-ff6kor0c	139	33	over	over	IN
cord-263987-ff6kor0c	139	34	some	some	DT
cord-263987-ff6kor0c	139	35	other	other	JJ
cord-263987-ff6kor0c	139	36	,	,	,
cord-263987-ff6kor0c	139	37	finite	finite	JJ
cord-263987-ff6kor0c	139	38	alphabet	alphabet	NN
cord-263987-ff6kor0c	139	39	)	)	-RRB-
cord-263987-ff6kor0c	139	40	.	.	.
cord-263987-ff6kor0c	140	1	Other	other	JJ
cord-263987-ff6kor0c	140	2	models	model	NNS
cord-263987-ff6kor0c	140	3	approximate	approximate	VBP
cord-263987-ff6kor0c	140	4	indels	indel	NNS
cord-263987-ff6kor0c	140	5	as	as	IN
cord-263987-ff6kor0c	140	6	a	a	DT
cord-263987-ff6kor0c	140	7	kind	kind	NN
cord-263987-ff6kor0c	140	8	of	of	IN
cord-263987-ff6kor0c	140	9	substitution	substitution	NN
cord-263987-ff6kor0c	140	10	that	that	WDT
cord-263987-ff6kor0c	140	11	temporarily	temporarily	RB
cord-263987-ff6kor0c	140	12	hides	hide	VBZ
cord-263987-ff6kor0c	140	13	a	a	DT
cord-263987-ff6kor0c	140	14	residue	residue	NN
cord-263987-ff6kor0c	140	15	,	,	,
cord-263987-ff6kor0c	140	16	by	by	IN
cord-263987-ff6kor0c	140	17	augmenting	augment	VBG
cord-263987-ff6kor0c	140	18	the	the	DT
cord-263987-ff6kor0c	140	19	DNA	dna	NN
cord-263987-ff6kor0c	140	20	or	or	CC
cord-263987-ff6kor0c	140	21	protein	protein	NN
cord-263987-ff6kor0c	140	22	alphabet	alphabet	NN
cord-263987-ff6kor0c	140	23	with	with	IN
cord-263987-ff6kor0c	140	24	an	an	DT
cord-263987-ff6kor0c	140	25	additional	additional	JJ
cord-263987-ff6kor0c	140	26	gap	gap	NN
cord-263987-ff6kor0c	140	27	character	character	NN
cord-263987-ff6kor0c	140	28	[	[	-LRB-
cord-263987-ff6kor0c	140	29	72	72	CD
cord-263987-ff6kor0c	140	30	]	]	-RRB-
cord-263987-ff6kor0c	140	31	[	[	-LRB-
cord-263987-ff6kor0c	140	32	73	73	CD
cord-263987-ff6kor0c	140	33	]	]	-RRB-
cord-263987-ff6kor0c	140	34	[	[	-LRB-
cord-263987-ff6kor0c	140	35	74	74	CD
cord-263987-ff6kor0c	140	36	]	]	-RRB-
cord-263987-ff6kor0c	140	37	.	.	.
cord-263987-ff6kor0c	141	1	These	these	DT
cord-263987-ff6kor0c	141	2	models	model	NNS
cord-263987-ff6kor0c	141	3	can	can	MD
cord-263987-ff6kor0c	141	4	be	be	VB
cord-263987-ff6kor0c	141	5	used	use	VBN
cord-263987-ff6kor0c	141	6	to	to	TO
cord-263987-ff6kor0c	141	7	calculate	calculate	VB
cord-263987-ff6kor0c	141	8	some	some	DT
cord-263987-ff6kor0c	141	9	form	form	NN
cord-263987-ff6kor0c	141	10	of	of	IN
cord-263987-ff6kor0c	141	11	likelihood	likelihood	NN
cord-263987-ff6kor0c	141	12	for	for	IN
cord-263987-ff6kor0c	141	13	a	a	DT
cord-263987-ff6kor0c	141	14	pairwise	pairwise	JJ
cord-263987-ff6kor0c	141	15	alignment	alignment	NN
cord-263987-ff6kor0c	141	16	of	of	IN
cord-263987-ff6kor0c	141	17	two	two	CD
cord-263987-ff6kor0c	141	18	sequences	sequence	NNS
cord-263987-ff6kor0c	141	19	,	,	,
cord-263987-ff6kor0c	141	20	but	but	CC
cord-263987-ff6kor0c	141	21	since	since	IN
cord-263987-ff6kor0c	141	22	this	this	DT
cord-263987-ff6kor0c	141	23	likelihood	likelihood	NN
cord-263987-ff6kor0c	141	24	is	be	VBZ
cord-263987-ff6kor0c	141	25	not	not	RB
cord-263987-ff6kor0c	141	26	derived	derive	VBN
cord-263987-ff6kor0c	141	27	from	from	IN
cord-263987-ff6kor0c	141	28	an	an	DT
cord-263987-ff6kor0c	141	29	underlying	underlie	VBG
cord-263987-ff6kor0c	141	30	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	141	31	model	model	NN
cord-263987-ff6kor0c	141	32	of	of	IN
cord-263987-ff6kor0c	141	33	indels	indel	NNS
cord-263987-ff6kor0c	141	34	,	,	,
cord-263987-ff6kor0c	141	35	the	the	DT
cord-263987-ff6kor0c	141	36	equations	equation	NNS
cord-263987-ff6kor0c	141	37	do	do	VBP
cord-263987-ff6kor0c	141	38	not	not	RB
cord-263987-ff6kor0c	141	39	,	,	,
cord-263987-ff6kor0c	141	40	in	in	IN
cord-263987-ff6kor0c	141	41	general	general	JJ
cord-263987-ff6kor0c	141	42	,	,	,
cord-263987-ff6kor0c	141	43	satisfy	satisfy	VB
cord-263987-ff6kor0c	141	44	the	the	DT
cord-263987-ff6kor0c	141	45	Chapman	Chapman	NNP
cord-263987-ff6kor0c	141	46	-	-	HYPH
cord-263987-ff6kor0c	141	47	Kolmogorov	Kolmogorov	NNP
cord-263987-ff6kor0c	141	48	forward	forward	RB
cord-263987-ff6kor0c	141	49	Eq	Eq	NNP
cord-263987-ff6kor0c	141	50	.	.	.
cord-263987-ff6kor0c	142	1	(	(	-LRB-
cord-263987-ff6kor0c	142	2	3	3	CD
cord-263987-ff6kor0c	142	3	)	)	-RRB-
cord-263987-ff6kor0c	142	4	.	.	.
cord-263987-ff6kor0c	143	1	That	that	RB
cord-263987-ff6kor0c	143	2	is	is	RB
cord-263987-ff6kor0c	143	3	,	,	,
cord-263987-ff6kor0c	143	4	the	the	DT
cord-263987-ff6kor0c	143	5	probability	probability	NN
cord-263987-ff6kor0c	143	6	of	of	IN
cord-263987-ff6kor0c	143	7	evolving	evolve	VBG
cord-263987-ff6kor0c	143	8	from	from	IN
cord-263987-ff6kor0c	143	9	i	i	PRP
cord-263987-ff6kor0c	143	10	to	to	IN
cord-263987-ff6kor0c	143	11	k	k	NNP
cord-263987-ff6kor0c	143	12	comes	come	VBZ
cord-263987-ff6kor0c	143	13	out	out	RP
cord-263987-ff6kor0c	143	14	differently	differently	RB
cord-263987-ff6kor0c	143	15	depending	depend	VBG
cord-263987-ff6kor0c	143	16	on	on	IN
cord-263987-ff6kor0c	143	17	whether	whether	IN
cord-263987-ff6kor0c	143	18	or	or	CC
cord-263987-ff6kor0c	143	19	not	not	RB
cord-263987-ff6kor0c	143	20	one	one	CD
cord-263987-ff6kor0c	143	21	conditions	condition	NNS
cord-263987-ff6kor0c	143	22	on	on	IN
cord-263987-ff6kor0c	143	23	an	an	DT
cord-263987-ff6kor0c	143	24	intermediate	intermediate	JJ
cord-263987-ff6kor0c	143	25	sequence	sequence	NN
cord-263987-ff6kor0c	144	1	j.	j.	NNP
cord-263987-ff6kor0c	144	2	Clearly	clearly	RB
cord-263987-ff6kor0c	144	3	,	,	,
cord-263987-ff6kor0c	144	4	something	something	NN
cord-263987-ff6kor0c	144	5	about	about	IN
cord-263987-ff6kor0c	144	6	this	this	DT
cord-263987-ff6kor0c	144	7	"	"	``
cord-263987-ff6kor0c	144	8	seems	seem	VBZ
cord-263987-ff6kor0c	144	9	wrong	wrong	JJ
cord-263987-ff6kor0c	144	10	"	"	''
cord-263987-ff6kor0c	144	11	:	:	:
cord-263987-ff6kor0c	144	12	the	the	DT
cord-263987-ff6kor0c	144	13	failure	failure	NN
cord-263987-ff6kor0c	144	14	to	to	TO
cord-263987-ff6kor0c	144	15	obey	obey	VB
cord-263987-ff6kor0c	144	16	Eq	Eq	NNP
cord-263987-ff6kor0c	144	17	.	.	.
cord-263987-ff6kor0c	145	1	3	3	CD
cord-263987-ff6kor0c	145	2	illustrates	illustrate	VBZ
cord-263987-ff6kor0c	145	3	the	the	DT
cord-263987-ff6kor0c	145	4	ad	ad	FW
cord-263987-ff6kor0c	145	5	hoc	hoc	FW
cord-263987-ff6kor0c	145	6	nature	nature	NN
cord-263987-ff6kor0c	145	7	of	of	IN
cord-263987-ff6kor0c	145	8	these	these	DT
cord-263987-ff6kor0c	145	9	approaches	approach	NNS
cord-263987-ff6kor0c	145	10	.	.	.
cord-263987-ff6kor0c	146	1	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	146	2	[	[	-LRB-
cord-263987-ff6kor0c	146	3	53	53	CD
cord-263987-ff6kor0c	146	4	]	]	-RRB-
cord-263987-ff6kor0c	146	5	describes	describe	VBZ
cord-263987-ff6kor0c	146	6	the	the	DT
cord-263987-ff6kor0c	146	7	Chapman	Chapman	NNP
cord-263987-ff6kor0c	146	8	-	-	HYPH
cord-263987-ff6kor0c	146	9	Kolmogorov	Kolmogorov	NNP
cord-263987-ff6kor0c	146	10	property	property	NN
cord-263987-ff6kor0c	146	11	(	(	-LRB-
cord-263987-ff6kor0c	146	12	Eq	Eq	NNP
cord-263987-ff6kor0c	146	13	.	.	NNP
cord-263987-ff6kor0c	146	14	3	3	LS
cord-263987-ff6kor0c	146	15	)	)	-RRB-
cord-263987-ff6kor0c	146	16	as	as	IN
cord-263987-ff6kor0c	146	17	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	146	18	consistency	consistency	NN
cord-263987-ff6kor0c	146	19	;	;	:
cord-263987-ff6kor0c	146	20	it	-PRON-	PRP
cord-263987-ff6kor0c	146	21	can	can	MD
cord-263987-ff6kor0c	146	22	also	also	RB
cord-263987-ff6kor0c	146	23	be	be	VB
cord-263987-ff6kor0c	146	24	regarded	regard	VBN
cord-263987-ff6kor0c	146	25	as	as	IN
cord-263987-ff6kor0c	146	26	being	be	VBG
cord-263987-ff6kor0c	146	27	the	the	DT
cord-263987-ff6kor0c	146	28	defining	define	VBG
cord-263987-ff6kor0c	146	29	property	property	NN
cord-263987-ff6kor0c	146	30	of	of	IN
cord-263987-ff6kor0c	146	31	any	any	DT
cord-263987-ff6kor0c	146	32	correct	correct	JJ
cord-263987-ff6kor0c	146	33	solution	solution	NN
cord-263987-ff6kor0c	146	34	to	to	IN
cord-263987-ff6kor0c	146	35	a	a	DT
cord-263987-ff6kor0c	146	36	continuous	continuous	JJ
cord-263987-ff6kor0c	146	37	-	-	HYPH
cord-263987-ff6kor0c	146	38	time	time	NN
cord-263987-ff6kor0c	146	39	Markov	Markov	NNP
cord-263987-ff6kor0c	146	40	chain	chain	NN
cord-263987-ff6kor0c	146	41	.	.	.
cord-263987-ff6kor0c	147	1	The	the	DT
cord-263987-ff6kor0c	147	2	abovementioned	abovementioned	JJ
cord-263987-ff6kor0c	147	3	approaches	approach	NNS
cord-263987-ff6kor0c	147	4	may	may	MD
cord-263987-ff6kor0c	147	5	be	be	VB
cord-263987-ff6kor0c	147	6	evolutionarily	evolutionarily	RB
cord-263987-ff6kor0c	147	7	consistent	consistent	JJ
cord-263987-ff6kor0c	147	8	if	if	IN
cord-263987-ff6kor0c	147	9	the	the	DT
cord-263987-ff6kor0c	147	10	state	state	NN
cord-263987-ff6kor0c	147	11	space	space	NN
cord-263987-ff6kor0c	147	12	is	be	VBZ
cord-263987-ff6kor0c	147	13	allowed	allow	VBN
cord-263987-ff6kor0c	147	14	to	to	TO
cord-263987-ff6kor0c	147	15	include	include	VB
cord-263987-ff6kor0c	147	16	the	the	DT
cord-263987-ff6kor0c	147	17	extra	extra	JJ
cord-263987-ff6kor0c	147	18	information	information	NN
cord-263987-ff6kor0c	147	19	that	that	WDT
cord-263987-ff6kor0c	147	20	is	be	VBZ
cord-263987-ff6kor0c	147	21	introduced	introduce	VBN
cord-263987-ff6kor0c	147	22	to	to	TO
cord-263987-ff6kor0c	147	23	make	make	VB
cord-263987-ff6kor0c	147	24	the	the	DT
cord-263987-ff6kor0c	147	25	model	model	NN
cord-263987-ff6kor0c	147	26	tractable	tractable	JJ
cord-263987-ff6kor0c	147	27	,	,	,
cord-263987-ff6kor0c	147	28	such	such	JJ
cord-263987-ff6kor0c	147	29	as	as	IN
cord-263987-ff6kor0c	147	30	fragment	fragment	NN
cord-263987-ff6kor0c	147	31	boundaries	boundary	NNS
cord-263987-ff6kor0c	147	32	.	.	.
cord-263987-ff6kor0c	148	1	Lèbre	Lèbre	NNP
cord-263987-ff6kor0c	148	2	and	and	CC
cord-263987-ff6kor0c	148	3	Michel	Michel	NNP
cord-263987-ff6kor0c	148	4	have	have	VBP
cord-263987-ff6kor0c	148	5	criticized	criticize	VBN
cord-263987-ff6kor0c	148	6	other	other	JJ
cord-263987-ff6kor0c	148	7	aspects	aspect	NNS
cord-263987-ff6kor0c	148	8	of	of	IN
cord-263987-ff6kor0c	148	9	the	the	DT
cord-263987-ff6kor0c	148	10	Rivas	Rivas	NNP
cord-263987-ff6kor0c	148	11	-	-	HYPH
cord-263987-ff6kor0c	148	12	Eddy	Eddy	NNP
cord-263987-ff6kor0c	148	13	2005	2005	CD
cord-263987-ff6kor0c	148	14	and	and	CC
cord-263987-ff6kor0c	148	15	2008	2008	CD
cord-263987-ff6kor0c	148	16	models	model	NNS
cord-263987-ff6kor0c	148	17	[	[	-LRB-
cord-263987-ff6kor0c	148	18	73	73	CD
cord-263987-ff6kor0c	148	19	,	,	,
cord-263987-ff6kor0c	148	20	74	74	CD
cord-263987-ff6kor0c	148	21	]	]	-RRB-
cord-263987-ff6kor0c	148	22	;	;	:
cord-263987-ff6kor0c	148	23	in	in	IN
cord-263987-ff6kor0c	148	24	particular	particular	JJ
cord-263987-ff6kor0c	148	25	,	,	,
cord-263987-ff6kor0c	148	26	incomplete	incomplete	JJ
cord-263987-ff6kor0c	148	27	separation	separation	NN
cord-263987-ff6kor0c	148	28	of	of	IN
cord-263987-ff6kor0c	148	29	the	the	DT
cord-263987-ff6kor0c	148	30	indel	indel	NN
cord-263987-ff6kor0c	148	31	and	and	CC
cord-263987-ff6kor0c	148	32	substitution	substitution	NN
cord-263987-ff6kor0c	148	33	processes	process	NNS
cord-263987-ff6kor0c	148	34	[	[	-LRB-
cord-263987-ff6kor0c	148	35	42	42	CD
cord-263987-ff6kor0c	148	36	]	]	-RRB-
cord-263987-ff6kor0c	148	37	.	.	.
cord-263987-ff6kor0c	149	1	Models	model	NNS
cord-263987-ff6kor0c	149	2	which	which	WDT
cord-263987-ff6kor0c	149	3	allow	allow	VBP
cord-263987-ff6kor0c	149	4	for	for	IN
cord-263987-ff6kor0c	149	5	heterogeneity	heterogeneity	NN
cord-263987-ff6kor0c	149	6	of	of	IN
cord-263987-ff6kor0c	149	7	indel	indel	NN
cord-263987-ff6kor0c	149	8	and	and	CC
cord-263987-ff6kor0c	149	9	substitution	substitution	NN
cord-263987-ff6kor0c	149	10	rates	rate	NNS
cord-263987-ff6kor0c	149	11	along	along	IN
cord-263987-ff6kor0c	149	12	the	the	DT
cord-263987-ff6kor0c	149	13	sequence	sequence	NN
cord-263987-ff6kor0c	149	14	also	also	RB
cord-263987-ff6kor0c	149	15	fall	fall	VBP
cord-263987-ff6kor0c	149	16	into	into	IN
cord-263987-ff6kor0c	149	17	this	this	DT
cord-263987-ff6kor0c	149	18	category	category	NN
cord-263987-ff6kor0c	149	19	of	of	IN
cord-263987-ff6kor0c	149	20	latent	latent	JJ
cord-263987-ff6kor0c	149	21	variable	variable	JJ
cord-263987-ff6kor0c	149	22	models	model	NNS
cord-263987-ff6kor0c	149	23	.	.	.
cord-263987-ff6kor0c	150	1	The	the	DT
cord-263987-ff6kor0c	150	2	usual	usual	JJ
cord-263987-ff6kor0c	150	3	way	way	NN
cord-263987-ff6kor0c	150	4	of	of	IN
cord-263987-ff6kor0c	150	5	allowing	allow	VBG
cord-263987-ff6kor0c	150	6	for	for	IN
cord-263987-ff6kor0c	150	7	such	such	JJ
cord-263987-ff6kor0c	150	8	spatial	spatial	JJ
cord-263987-ff6kor0c	150	9	variation	variation	NN
cord-263987-ff6kor0c	150	10	in	in	IN
cord-263987-ff6kor0c	150	11	substitution	substitution	NN
cord-263987-ff6kor0c	150	12	models	model	NNS
cord-263987-ff6kor0c	150	13	is	be	VBZ
cord-263987-ff6kor0c	150	14	to	to	TO
cord-263987-ff6kor0c	150	15	assume	assume	VB
cord-263987-ff6kor0c	150	16	a	a	DT
cord-263987-ff6kor0c	150	17	latent	latent	JJ
cord-263987-ff6kor0c	150	18	rate	rate	NN
cord-263987-ff6kor0c	150	19	-	-	HYPH
cord-263987-ff6kor0c	150	20	scaling	scale	VBG
cord-263987-ff6kor0c	150	21	parameter	parameter	NN
cord-263987-ff6kor0c	150	22	associated	associate	VBN
cord-263987-ff6kor0c	150	23	with	with	IN
cord-263987-ff6kor0c	150	24	each	each	DT
cord-263987-ff6kor0c	150	25	site	site	NN
cord-263987-ff6kor0c	150	26	[	[	-LRB-
cord-263987-ff6kor0c	150	27	4	4	CD
cord-263987-ff6kor0c	150	28	,	,	,
cord-263987-ff6kor0c	150	29	5	5	CD
cord-263987-ff6kor0c	150	30	]	]	-RRB-
cord-263987-ff6kor0c	150	31	.	.	.
cord-263987-ff6kor0c	151	1	For	for	IN
cord-263987-ff6kor0c	151	2	indel	indel	NN
cord-263987-ff6kor0c	151	3	models	model	NNS
cord-263987-ff6kor0c	151	4	,	,	,
cord-263987-ff6kor0c	151	5	this	this	DT
cord-263987-ff6kor0c	151	6	latent	latent	JJ
cord-263987-ff6kor0c	151	7	information	information	NN
cord-263987-ff6kor0c	151	8	must	must	MD
cord-263987-ff6kor0c	151	9	be	be	VB
cord-263987-ff6kor0c	151	10	extended	extend	VBN
cord-263987-ff6kor0c	151	11	to	to	TO
cord-263987-ff6kor0c	151	12	include	include	VB
cord-263987-ff6kor0c	151	13	hidden	hide	VBN
cord-263987-ff6kor0c	151	14	site	site	NN
cord-263987-ff6kor0c	151	15	boundaries	boundary	NNS
cord-263987-ff6kor0c	151	16	[	[	-LRB-
cord-263987-ff6kor0c	151	17	56	56	CD
cord-263987-ff6kor0c	151	18	]	]	-RRB-
cord-263987-ff6kor0c	151	19	.	.	.
cord-263987-ff6kor0c	152	1	Another	another	DT
cord-263987-ff6kor0c	152	2	variation	variation	NN
cord-263987-ff6kor0c	152	3	on	on	IN
cord-263987-ff6kor0c	152	4	TKF91	TKF91	NNP
cord-263987-ff6kor0c	152	5	is	be	VBZ
cord-263987-ff6kor0c	152	6	the	the	DT
cord-263987-ff6kor0c	152	7	TKF	TKF	NNP
cord-263987-ff6kor0c	152	8	Structure	Structure	NNP
cord-263987-ff6kor0c	152	9	Tree	Tree	NNP
cord-263987-ff6kor0c	152	10	,	,	,
cord-263987-ff6kor0c	152	11	which	which	WDT
cord-263987-ff6kor0c	152	12	describes	describe	VBZ
cord-263987-ff6kor0c	152	13	the	the	DT
cord-263987-ff6kor0c	152	14	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	152	15	behavior	behavior	NN
cord-263987-ff6kor0c	152	16	of	of	IN
cord-263987-ff6kor0c	152	17	RNA	RNA	NNP
cord-263987-ff6kor0c	152	18	structures	structure	NNS
cord-263987-ff6kor0c	152	19	with	with	IN
cord-263987-ff6kor0c	152	20	stem	stem	NN
cord-263987-ff6kor0c	152	21	and	and	CC
cord-263987-ff6kor0c	152	22	loop	loop	NN
cord-263987-ff6kor0c	152	23	regions	region	NNS
cord-263987-ff6kor0c	152	24	which	which	WDT
cord-263987-ff6kor0c	152	25	are	be	VBP
cord-263987-ff6kor0c	152	26	subject	subject	JJ
cord-263987-ff6kor0c	152	27	to	to	IN
cord-263987-ff6kor0c	152	28	insertion	insertion	NN
cord-263987-ff6kor0c	152	29	and	and	CC
cord-263987-ff6kor0c	152	30	deletion	deletion	NN
cord-263987-ff6kor0c	152	31	[	[	-LRB-
cord-263987-ff6kor0c	152	32	75	75	CD
cord-263987-ff6kor0c	152	33	]	]	-RRB-
cord-263987-ff6kor0c	152	34	.	.	.
cord-263987-ff6kor0c	153	1	Rather	rather	RB
cord-263987-ff6kor0c	153	2	than	than	IN
cord-263987-ff6kor0c	153	3	describing	describe	VBG
cord-263987-ff6kor0c	153	4	the	the	DT
cord-263987-ff6kor0c	153	5	evolution	evolution	NN
cord-263987-ff6kor0c	153	6	of	of	IN
cord-263987-ff6kor0c	153	7	a	a	DT
cord-263987-ff6kor0c	153	8	sequence	sequence	NN
cord-263987-ff6kor0c	153	9	,	,	,
cord-263987-ff6kor0c	153	10	this	this	DT
cord-263987-ff6kor0c	153	11	model	model	NN
cord-263987-ff6kor0c	153	12	essentially	essentially	RB
cord-263987-ff6kor0c	153	13	captures	capture	VBZ
cord-263987-ff6kor0c	153	14	the	the	DT
cord-263987-ff6kor0c	153	15	time	time	NN
cord-263987-ff6kor0c	153	16	-	-	HYPH
cord-263987-ff6kor0c	153	17	evolution	evolution	NN
cord-263987-ff6kor0c	153	18	grammar	grammar	NN
cord-263987-ff6kor0c	153	19	of	of	IN
cord-263987-ff6kor0c	153	20	a	a	DT
cord-263987-ff6kor0c	153	21	tree	tree	NN
cord-263987-ff6kor0c	153	22	-	-	HYPH
cord-263987-ff6kor0c	153	23	like	like	JJ
cord-263987-ff6kor0c	153	24	graph	graph	NN
cord-263987-ff6kor0c	153	25	whose	whose	WP$
cord-263987-ff6kor0c	153	26	individual	individual	JJ
cord-263987-ff6kor0c	153	27	edges	edge	NNS
cord-263987-ff6kor0c	153	28	are	be	VBP
cord-263987-ff6kor0c	153	29	evolving	evolve	VBG
cord-263987-ff6kor0c	153	30	according	accord	VBG
cord-263987-ff6kor0c	153	31	to	to	IN
cord-263987-ff6kor0c	153	32	the	the	DT
cord-263987-ff6kor0c	153	33	TKF91	TKF91	NNP
cord-263987-ff6kor0c	153	34	model	model	NN
cord-263987-ff6kor0c	153	35	.	.	.
cord-263987-ff6kor0c	154	1	Other	other	JJ
cord-263987-ff6kor0c	154	2	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	154	3	models	model	NNS
cord-263987-ff6kor0c	154	4	have	have	VBP
cord-263987-ff6kor0c	154	5	made	make	VBN
cord-263987-ff6kor0c	154	6	use	use	NN
cord-263987-ff6kor0c	154	7	of	of	IN
cord-263987-ff6kor0c	154	8	graph	graph	NN
cord-263987-ff6kor0c	154	9	grammars	grammar	NNS
cord-263987-ff6kor0c	154	10	,	,	,
cord-263987-ff6kor0c	154	11	for	for	IN
cord-263987-ff6kor0c	154	12	example	example	NN
cord-263987-ff6kor0c	154	13	to	to	TO
cord-263987-ff6kor0c	154	14	model	model	NN
cord-263987-ff6kor0c	154	15	pseudoknots	pseudoknot	NNS
cord-263987-ff6kor0c	154	16	[	[	-LRB-
cord-263987-ff6kor0c	154	17	76	76	CD
cord-263987-ff6kor0c	154	18	]	]	-RRB-
cord-263987-ff6kor0c	154	19	or	or	CC
cord-263987-ff6kor0c	154	20	context	context	NN
cord-263987-ff6kor0c	154	21	-	-	HYPH
cord-263987-ff6kor0c	154	22	dependent	dependent	JJ
cord-263987-ff6kor0c	154	23	indels	indel	NNS
cord-263987-ff6kor0c	154	24	[	[	-LRB-
cord-263987-ff6kor0c	154	25	77	77	CD
cord-263987-ff6kor0c	154	26	]	]	-RRB-
cord-263987-ff6kor0c	154	27	.	.	.
cord-263987-ff6kor0c	155	1	In	in	IN
cord-263987-ff6kor0c	155	2	tackling	tackle	VBG
cord-263987-ff6kor0c	155	3	indel	indel	NN
cord-263987-ff6kor0c	155	4	models	model	NNS
cord-263987-ff6kor0c	155	5	where	where	WRB
cord-263987-ff6kor0c	155	6	the	the	DT
cord-263987-ff6kor0c	155	7	indel	indel	NN
cord-263987-ff6kor0c	155	8	events	event	NNS
cord-263987-ff6kor0c	155	9	can	can	MD
cord-263987-ff6kor0c	155	10	insert	insert	VB
cord-263987-ff6kor0c	155	11	or	or	CC
cord-263987-ff6kor0c	155	12	delete	delete	VB
cord-263987-ff6kor0c	155	13	multiple	multiple	JJ
cord-263987-ff6kor0c	155	14	residues	residue	NNS
cord-263987-ff6kor0c	155	15	at	at	IN
cord-263987-ff6kor0c	155	16	once	once	RB
cord-263987-ff6kor0c	155	17	,	,	,
cord-263987-ff6kor0c	155	18	several	several	JJ
cord-263987-ff6kor0c	155	19	authors	author	NNS
cord-263987-ff6kor0c	155	20	have	have	VBP
cord-263987-ff6kor0c	155	21	used	use	VBN
cord-263987-ff6kor0c	155	22	the	the	DT
cord-263987-ff6kor0c	155	23	approximation	approximation	NN
cord-263987-ff6kor0c	155	24	that	that	IN
cord-263987-ff6kor0c	155	25	indels	indel	NNS
cord-263987-ff6kor0c	155	26	never	never	RB
cord-263987-ff6kor0c	155	27	overlap	overlap	VBP
cord-263987-ff6kor0c	155	28	,	,	,
cord-263987-ff6kor0c	155	29	so	so	IN
cord-263987-ff6kor0c	155	30	that	that	IN
cord-263987-ff6kor0c	155	31	any	any	DT
cord-263987-ff6kor0c	155	32	observed	observed	JJ
cord-263987-ff6kor0c	155	33	gap	gap	NN
cord-263987-ff6kor0c	155	34	corresponds	correspond	VBZ
cord-263987-ff6kor0c	155	35	to	to	IN
cord-263987-ff6kor0c	155	36	a	a	DT
cord-263987-ff6kor0c	155	37	single	single	JJ
cord-263987-ff6kor0c	155	38	indel	indel	NN
cord-263987-ff6kor0c	155	39	event	event	NN
cord-263987-ff6kor0c	155	40	.	.	.
cord-263987-ff6kor0c	156	1	This	this	DT
cord-263987-ff6kor0c	156	2	approximation	approximation	NN
cord-263987-ff6kor0c	156	3	,	,	,
cord-263987-ff6kor0c	156	4	which	which	WDT
cord-263987-ff6kor0c	156	5	is	be	VBZ
cord-263987-ff6kor0c	156	6	justified	justify	VBN
cord-263987-ff6kor0c	156	7	if	if	IN
cord-263987-ff6kor0c	156	8	one	one	CD
cord-263987-ff6kor0c	156	9	is	be	VBZ
cord-263987-ff6kor0c	156	10	considering	consider	VBG
cord-263987-ff6kor0c	156	11	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	156	12	timespans	timespan	NNS
cord-263987-ff6kor0c	156	13	t	t	NNP
cord-263987-ff6kor0c	156	14	1/(δ	1/(δ	CD
cord-263987-ff6kor0c	156	15	)	)	-RRB-
cord-263987-ff6kor0c	156	16	where	where	WRB
cord-263987-ff6kor0c	156	17	δ	δ	NNP
cord-263987-ff6kor0c	156	18	is	be	VBZ
cord-263987-ff6kor0c	156	19	the	the	DT
cord-263987-ff6kor0c	156	20	indel	indel	NN
cord-263987-ff6kor0c	156	21	rate	rate	NN
cord-263987-ff6kor0c	156	22	per	per	IN
cord-263987-ff6kor0c	156	23	site	site	NN
cord-263987-ff6kor0c	156	24	and	and	CC
cord-263987-ff6kor0c	156	25	is	be	VBZ
cord-263987-ff6kor0c	156	26	the	the	DT
cord-263987-ff6kor0c	156	27	gap	gap	NN
cord-263987-ff6kor0c	156	28	length	length	NN
cord-263987-ff6kor0c	156	29	,	,	,
cord-263987-ff6kor0c	156	30	considerably	considerably	RB
cord-263987-ff6kor0c	156	31	simplifies	simplify	VBZ
cord-263987-ff6kor0c	156	32	the	the	DT
cord-263987-ff6kor0c	156	33	task	task	NN
cord-263987-ff6kor0c	156	34	of	of	IN
cord-263987-ff6kor0c	156	35	calculating	calculate	VBG
cord-263987-ff6kor0c	156	36	gap	gap	NN
cord-263987-ff6kor0c	156	37	probabilities	probability	NNS
cord-263987-ff6kor0c	156	38	[	[	-LRB-
cord-263987-ff6kor0c	156	39	67	67	CD
cord-263987-ff6kor0c	156	40	,	,	,
cord-263987-ff6kor0c	156	41	[	[	-LRB-
cord-263987-ff6kor0c	156	42	78	78	CD
cord-263987-ff6kor0c	156	43	]	]	-RRB-
cord-263987-ff6kor0c	156	44	[	[	-LRB-
cord-263987-ff6kor0c	156	45	79	79	CD
cord-263987-ff6kor0c	156	46	]	]	-RRB-
cord-263987-ff6kor0c	156	47	[	[	-LRB-
cord-263987-ff6kor0c	156	48	80	80	CD
cord-263987-ff6kor0c	156	49	]	]	-RRB-
cord-263987-ff6kor0c	156	50	[	[	-LRB-
cord-263987-ff6kor0c	156	51	81	81	CD
cord-263987-ff6kor0c	156	52	]	]	-RRB-
cord-263987-ff6kor0c	156	53	[	[	-LRB-
cord-263987-ff6kor0c	156	54	82	82	CD
cord-263987-ff6kor0c	156	55	]	]	-RRB-
cord-263987-ff6kor0c	156	56	[	[	-LRB-
cord-263987-ff6kor0c	156	57	83	83	CD
cord-263987-ff6kor0c	156	58	]	]	-RRB-
cord-263987-ff6kor0c	156	59	.	.	.
cord-263987-ff6kor0c	157	1	At	at	IN
cord-263987-ff6kor0c	157	2	longer	long	JJR
cord-263987-ff6kor0c	157	3	timescales	timescale	NNS
cord-263987-ff6kor0c	157	4	,	,	,
cord-263987-ff6kor0c	157	5	it	-PRON-	PRP
cord-263987-ff6kor0c	157	6	is	be	VBZ
cord-263987-ff6kor0c	157	7	necessary	necessary	JJ
cord-263987-ff6kor0c	157	8	to	to	TO
cord-263987-ff6kor0c	157	9	consider	consider	VB
cord-263987-ff6kor0c	157	10	multiple	multiple	JJ
cord-263987-ff6kor0c	157	11	-	-	HYPH
cord-263987-ff6kor0c	157	12	event	event	NN
cord-263987-ff6kor0c	157	13	trajectories	trajectory	NNS
cord-263987-ff6kor0c	157	14	,	,	,
cord-263987-ff6kor0c	157	15	but	but	CC
cord-263987-ff6kor0c	157	16	(	(	-LRB-
cord-263987-ff6kor0c	157	17	as	as	IN
cord-263987-ff6kor0c	157	18	a	a	DT
cord-263987-ff6kor0c	157	19	simplifying	simplify	VBG
cord-263987-ff6kor0c	157	20	approximation	approximation	NN
cord-263987-ff6kor0c	157	21	)	)	-RRB-
cord-263987-ff6kor0c	157	22	one	one	PRP
cord-263987-ff6kor0c	157	23	can	can	MD
cord-263987-ff6kor0c	157	24	still	still	RB
cord-263987-ff6kor0c	157	25	truncate	truncate	VB
cord-263987-ff6kor0c	157	26	the	the	DT
cord-263987-ff6kor0c	157	27	trajectory	trajectory	NN
cord-263987-ff6kor0c	157	28	at	at	IN
cord-263987-ff6kor0c	157	29	a	a	DT
cord-263987-ff6kor0c	157	30	finite	finite	JJ
cord-263987-ff6kor0c	157	31	number	number	NN
cord-263987-ff6kor0c	157	32	of	of	IN
cord-263987-ff6kor0c	157	33	events	event	NNS
cord-263987-ff6kor0c	157	34	.	.	.
cord-263987-ff6kor0c	158	1	A	a	DT
cord-263987-ff6kor0c	158	2	problem	problem	NN
cord-263987-ff6kor0c	158	3	with	with	IN
cord-263987-ff6kor0c	158	4	this	this	DT
cord-263987-ff6kor0c	158	5	approach	approach	NN
cord-263987-ff6kor0c	158	6	is	be	VBZ
cord-263987-ff6kor0c	158	7	that	that	IN
cord-263987-ff6kor0c	158	8	many	many	JJ
cord-263987-ff6kor0c	158	9	different	different	JJ
cord-263987-ff6kor0c	158	10	trajectories	trajectory	NNS
cord-263987-ff6kor0c	158	11	will	will	MD
cord-263987-ff6kor0c	158	12	generally	generally	RB
cord-263987-ff6kor0c	158	13	be	be	VB
cord-263987-ff6kor0c	158	14	consistent	consistent	JJ
cord-263987-ff6kor0c	158	15	with	with	IN
cord-263987-ff6kor0c	158	16	an	an	DT
cord-263987-ff6kor0c	158	17	observed	observed	JJ
cord-263987-ff6kor0c	158	18	mutation	mutation	NN
cord-263987-ff6kor0c	158	19	.	.	.
cord-263987-ff6kor0c	159	1	Summing	sum	VBG
cord-263987-ff6kor0c	159	2	over	over	IN
cord-263987-ff6kor0c	159	3	all	all	DT
cord-263987-ff6kor0c	159	4	such	such	JJ
cord-263987-ff6kor0c	159	5	trajectories	trajectory	NNS
cord-263987-ff6kor0c	159	6	,	,	,
cord-263987-ff6kor0c	159	7	to	to	TO
cord-263987-ff6kor0c	159	8	compute	compute	VB
cord-263987-ff6kor0c	159	9	the	the	DT
cord-263987-ff6kor0c	159	10	probability	probability	NN
cord-263987-ff6kor0c	159	11	of	of	IN
cord-263987-ff6kor0c	159	12	observing	observe	VBG
cord-263987-ff6kor0c	159	13	a	a	DT
cord-263987-ff6kor0c	159	14	particular	particular	JJ
cord-263987-ff6kor0c	159	15	configuration	configuration	NN
cord-263987-ff6kor0c	159	16	after	after	IN
cord-263987-ff6kor0c	159	17	finite	finite	JJ
cord-263987-ff6kor0c	159	18	time	time	NN
cord-263987-ff6kor0c	159	19	(	(	-LRB-
cord-263987-ff6kor0c	159	20	e.g.	e.g.	RB
cord-263987-ff6kor0c	159	21	the	the	DT
cord-263987-ff6kor0c	159	22	observed	observed	JJ
cord-263987-ff6kor0c	159	23	gap	gap	NN
cord-263987-ff6kor0c	159	24	length	length	NN
cord-263987-ff6kor0c	159	25	distribution	distribution	NN
cord-263987-ff6kor0c	159	26	)	)	-RRB-
cord-263987-ff6kor0c	159	27	,	,	,
cord-263987-ff6kor0c	159	28	is	be	VBZ
cord-263987-ff6kor0c	159	29	a	a	DT
cord-263987-ff6kor0c	159	30	nontrivial	nontrivial	JJ
cord-263987-ff6kor0c	159	31	problem	problem	NN
cord-263987-ff6kor0c	159	32	.	.	.
cord-263987-ff6kor0c	160	1	In	in	IN
cord-263987-ff6kor0c	160	2	analyzing	analyze	VBG
cord-263987-ff6kor0c	160	3	the	the	DT
cord-263987-ff6kor0c	160	4	long	long	JJ
cord-263987-ff6kor0c	160	5	indel	indel	NN
cord-263987-ff6kor0c	160	6	model	model	NN
cord-263987-ff6kor0c	160	7	,	,	,
cord-263987-ff6kor0c	160	8	a	a	DT
cord-263987-ff6kor0c	160	9	generalization	generalization	NN
cord-263987-ff6kor0c	160	10	of	of	IN
cord-263987-ff6kor0c	160	11	TKF91	TKF91	NNP
cord-263987-ff6kor0c	160	12	with	with	IN
cord-263987-ff6kor0c	160	13	arbitrary	arbitrary	JJ
cord-263987-ff6kor0c	160	14	length	length	NN
cord-263987-ff6kor0c	160	15	distributions	distribution	NNS
cord-263987-ff6kor0c	160	16	for	for	IN
cord-263987-ff6kor0c	160	17	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	160	18	indel	indel	NN
cord-263987-ff6kor0c	160	19	events	event	NNS
cord-263987-ff6kor0c	160	20	,	,	,
cord-263987-ff6kor0c	160	21	Miklós	Miklós	NNP
cord-263987-ff6kor0c	160	22	et	et	NNP
cord-263987-ff6kor0c	160	23	al	al	NNP
cord-263987-ff6kor0c	160	24	.	.	.
cord-263987-ff6kor0c	161	1	[	[	-LRB-
cord-263987-ff6kor0c	161	2	84	84	CD
cord-263987-ff6kor0c	161	3	]	]	-RRB-
cord-263987-ff6kor0c	161	4	make	make	VB
cord-263987-ff6kor0c	161	5	the	the	DT
cord-263987-ff6kor0c	161	6	claim	claim	NN
cord-263987-ff6kor0c	161	7	that	that	IN
cord-263987-ff6kor0c	161	8	the	the	DT
cord-263987-ff6kor0c	161	9	existence	existence	NN
cord-263987-ff6kor0c	161	10	of	of	IN
cord-263987-ff6kor0c	161	11	a	a	DT
cord-263987-ff6kor0c	161	12	conserved	conserved	JJ
cord-263987-ff6kor0c	161	13	residue	residue	NN
cord-263987-ff6kor0c	161	14	implies	imply	VBZ
cord-263987-ff6kor0c	161	15	the	the	DT
cord-263987-ff6kor0c	161	16	alignment	alignment	NN
cord-263987-ff6kor0c	161	17	probability	probability	NN
cord-263987-ff6kor0c	161	18	is	be	VBZ
cord-263987-ff6kor0c	161	19	factorable	factorable	JJ
cord-263987-ff6kor0c	161	20	at	at	IN
cord-263987-ff6kor0c	161	21	that	that	DT
cord-263987-ff6kor0c	161	22	point	point	NN
cord-263987-ff6kor0c	161	23	(	(	-LRB-
cord-263987-ff6kor0c	161	24	since	since	IN
cord-263987-ff6kor0c	161	25	no	no	DT
cord-263987-ff6kor0c	161	26	indel	indel	NN
cord-263987-ff6kor0c	161	27	has	have	VBZ
cord-263987-ff6kor0c	161	28	ever	ever	RB
cord-263987-ff6kor0c	161	29	crossed	cross	VBN
cord-263987-ff6kor0c	161	30	the	the	DT
cord-263987-ff6kor0c	161	31	boundary	boundary	NN
cord-263987-ff6kor0c	161	32	)	)	-RRB-
cord-263987-ff6kor0c	161	33	.	.	.
cord-263987-ff6kor0c	162	1	They	-PRON-	PRP
cord-263987-ff6kor0c	162	2	use	use	VBP
cord-263987-ff6kor0c	162	3	a	a	DT
cord-263987-ff6kor0c	162	4	numerical	numerical	JJ
cord-263987-ff6kor0c	162	5	sum	sum	NN
cord-263987-ff6kor0c	162	6	over	over	IN
cord-263987-ff6kor0c	162	7	indel	indel	NN
cord-263987-ff6kor0c	162	8	trajectories	trajectory	NNS
cord-263987-ff6kor0c	162	9	to	to	TO
cord-263987-ff6kor0c	162	10	approximate	approximate	VB
cord-263987-ff6kor0c	162	11	the	the	DT
cord-263987-ff6kor0c	162	12	probability	probability	NN
cord-263987-ff6kor0c	162	13	distribution	distribution	NN
cord-263987-ff6kor0c	162	14	of	of	IN
cord-263987-ff6kor0c	162	15	observed	observed	JJ
cord-263987-ff6kor0c	162	16	gap	gap	NN
cord-263987-ff6kor0c	162	17	lengths	length	NNS
cord-263987-ff6kor0c	162	18	.	.	.
cord-263987-ff6kor0c	163	1	Although	although	IN
cord-263987-ff6kor0c	163	2	they	-PRON-	PRP
cord-263987-ff6kor0c	163	3	used	use	VBD
cord-263987-ff6kor0c	163	4	a	a	DT
cord-263987-ff6kor0c	163	5	reversible	reversible	JJ
cord-263987-ff6kor0c	163	6	model	model	NN
cord-263987-ff6kor0c	163	7	,	,	,
cord-263987-ff6kor0c	163	8	their	-PRON-	PRP$
cord-263987-ff6kor0c	163	9	approach	approach	NN
cord-263987-ff6kor0c	163	10	generalizes	generalize	VBZ
cord-263987-ff6kor0c	163	11	readily	readily	RB
cord-263987-ff6kor0c	163	12	to	to	IN
cord-263987-ff6kor0c	163	13	irreversible	irreversible	JJ
cord-263987-ff6kor0c	163	14	models	model	NNS
cord-263987-ff6kor0c	163	15	.	.	.
cord-263987-ff6kor0c	164	1	This	this	DT
cord-263987-ff6kor0c	164	2	work	work	NN
cord-263987-ff6kor0c	164	3	builds	build	VBZ
cord-263987-ff6kor0c	164	4	on	on	IN
cord-263987-ff6kor0c	164	5	an	an	DT
cord-263987-ff6kor0c	164	6	earlier	early	JJR
cord-263987-ff6kor0c	164	7	model	model	NN
cord-263987-ff6kor0c	164	8	which	which	WDT
cord-263987-ff6kor0c	164	9	allows	allow	VBZ
cord-263987-ff6kor0c	164	10	long	long	JJ
cord-263987-ff6kor0c	164	11	insertions	insertion	NNS
cord-263987-ff6kor0c	164	12	,	,	,
cord-263987-ff6kor0c	164	13	but	but	CC
cord-263987-ff6kor0c	164	14	only	only	RB
cord-263987-ff6kor0c	164	15	single	single	JJ
cord-263987-ff6kor0c	164	16	-	-	HYPH
cord-263987-ff6kor0c	164	17	residue	residue	NN
cord-263987-ff6kor0c	164	18	deletions	deletion	NNS
cord-263987-ff6kor0c	164	19	[	[	-LRB-
cord-263987-ff6kor0c	164	20	85	85	CD
cord-263987-ff6kor0c	164	21	]	]	-RRB-
cord-263987-ff6kor0c	164	22	.	.	.
cord-263987-ff6kor0c	165	1	Recent	recent	JJ
cord-263987-ff6kor0c	165	2	work	work	NN
cord-263987-ff6kor0c	165	3	by	by	IN
cord-263987-ff6kor0c	165	4	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	165	5	has	have	VBZ
cord-263987-ff6kor0c	165	6	put	put	VBN
cord-263987-ff6kor0c	165	7	this	this	DT
cord-263987-ff6kor0c	165	8	finite	finite	JJ
cord-263987-ff6kor0c	165	9	-	-	HYPH
cord-263987-ff6kor0c	165	10	event	event	NN
cord-263987-ff6kor0c	165	11	approximation	approximation	NN
cord-263987-ff6kor0c	165	12	on	on	IN
cord-263987-ff6kor0c	165	13	a	a	DT
cord-263987-ff6kor0c	165	14	more	more	RBR
cord-263987-ff6kor0c	165	15	solid	solid	JJ
cord-263987-ff6kor0c	165	16	footing	footing	NN
cord-263987-ff6kor0c	165	17	by	by	IN
cord-263987-ff6kor0c	165	18	developing	develop	VBG
cord-263987-ff6kor0c	165	19	a	a	DT
cord-263987-ff6kor0c	165	20	rigorous	rigorous	JJ
cord-263987-ff6kor0c	165	21	algebraic	algebraic	JJ
cord-263987-ff6kor0c	165	22	definition	definition	NN
cord-263987-ff6kor0c	165	23	of	of	IN
cord-263987-ff6kor0c	165	24	equivalence	equivalence	NN
cord-263987-ff6kor0c	165	25	classes	class	NNS
cord-263987-ff6kor0c	165	26	for	for	IN
cord-263987-ff6kor0c	165	27	event	event	NN
cord-263987-ff6kor0c	165	28	trajectories	trajectory	NNS
cord-263987-ff6kor0c	165	29	[	[	-LRB-
cord-263987-ff6kor0c	165	30	53	53	CD
cord-263987-ff6kor0c	165	31	]	]	-RRB-
cord-263987-ff6kor0c	165	32	[	[	-LRB-
cord-263987-ff6kor0c	165	33	54	54	CD
cord-263987-ff6kor0c	165	34	]	]	-RRB-
cord-263987-ff6kor0c	165	35	[	[	-LRB-
cord-263987-ff6kor0c	165	36	55	55	CD
cord-263987-ff6kor0c	165	37	]	]	-RRB-
cord-263987-ff6kor0c	165	38	.	.	.
cord-263987-ff6kor0c	166	1	Solutions	solution	NNS
cord-263987-ff6kor0c	166	2	obtained	obtain	VBN
cord-263987-ff6kor0c	166	3	using	use	VBG
cord-263987-ff6kor0c	166	4	finite	finite	JJ
cord-263987-ff6kor0c	166	5	-	-	HYPH
cord-263987-ff6kor0c	166	6	event	event	NN
cord-263987-ff6kor0c	166	7	approximations	approximation	NNS
cord-263987-ff6kor0c	166	8	will	will	MD
cord-263987-ff6kor0c	166	9	not	not	RB
cord-263987-ff6kor0c	166	10	exactly	exactly	RB
cord-263987-ff6kor0c	166	11	satisfy	satisfy	VB
cord-263987-ff6kor0c	166	12	Eq	Eq	NNP
cord-263987-ff6kor0c	166	13	.	.	.
cord-263987-ff6kor0c	167	1	3	3	LS
cord-263987-ff6kor0c	167	2	.	.	.
cord-263987-ff6kor0c	168	1	There	there	EX
cord-263987-ff6kor0c	168	2	will	will	MD
cord-263987-ff6kor0c	168	3	be	be	VB
cord-263987-ff6kor0c	168	4	some	some	DT
cord-263987-ff6kor0c	168	5	error	error	NN
cord-263987-ff6kor0c	168	6	in	in	IN
cord-263987-ff6kor0c	168	7	the	the	DT
cord-263987-ff6kor0c	168	8	probability	probability	NN
cord-263987-ff6kor0c	168	9	,	,	,
cord-263987-ff6kor0c	168	10	and	and	CC
cord-263987-ff6kor0c	168	11	in	in	IN
cord-263987-ff6kor0c	168	12	general	general	JJ
cord-263987-ff6kor0c	168	13	the	the	DT
cord-263987-ff6kor0c	168	14	error	error	NN
cord-263987-ff6kor0c	168	15	will	will	MD
cord-263987-ff6kor0c	168	16	be	be	VB
cord-263987-ff6kor0c	168	17	greater	great	JJR
cord-263987-ff6kor0c	168	18	on	on	IN
cord-263987-ff6kor0c	168	19	longer	long	JJR
cord-263987-ff6kor0c	168	20	branches	branch	NNS
cord-263987-ff6kor0c	168	21	,	,	,
cord-263987-ff6kor0c	168	22	as	as	IN
cord-263987-ff6kor0c	168	23	the	the	DT
cord-263987-ff6kor0c	168	24	main	main	JJ
cord-263987-ff6kor0c	168	25	assumption	assumption	NN
cord-263987-ff6kor0c	168	26	behind	behind	IN
cord-263987-ff6kor0c	168	27	the	the	DT
cord-263987-ff6kor0c	168	28	approximation	approximation	NN
cord-263987-ff6kor0c	169	1	(	(	-LRB-
cord-263987-ff6kor0c	169	2	that	that	IN
cord-263987-ff6kor0c	169	3	there	there	EX
cord-263987-ff6kor0c	169	4	are	be	VBP
cord-263987-ff6kor0c	169	5	no	no	DT
cord-263987-ff6kor0c	169	6	overlapping	overlap	VBG
cord-263987-ff6kor0c	169	7	indels	indel	NNS
cord-263987-ff6kor0c	169	8	in	in	IN
cord-263987-ff6kor0c	169	9	the	the	DT
cord-263987-ff6kor0c	169	10	time	time	NN
cord-263987-ff6kor0c	169	11	interval	interval	NN
cord-263987-ff6kor0c	169	12	,	,	,
cord-263987-ff6kor0c	169	13	or	or	CC
cord-263987-ff6kor0c	169	14	that	that	IN
cord-263987-ff6kor0c	169	15	there	there	EX
cord-263987-ff6kor0c	169	16	is	be	VBZ
cord-263987-ff6kor0c	169	17	a	a	DT
cord-263987-ff6kor0c	169	18	finite	finite	JJ
cord-263987-ff6kor0c	169	19	limit	limit	NN
cord-263987-ff6kor0c	169	20	to	to	IN
cord-263987-ff6kor0c	169	21	the	the	DT
cord-263987-ff6kor0c	169	22	number	number	NN
cord-263987-ff6kor0c	169	23	of	of	IN
cord-263987-ff6kor0c	169	24	overlapping	overlap	VBG
cord-263987-ff6kor0c	169	25	indels	indel	NNS
cord-263987-ff6kor0c	169	26	)	)	-RRB-
cord-263987-ff6kor0c	169	27	starts	start	VBZ
cord-263987-ff6kor0c	169	28	to	to	TO
cord-263987-ff6kor0c	169	29	break	break	VB
cord-263987-ff6kor0c	169	30	down	down	RP
cord-263987-ff6kor0c	169	31	.	.	.
cord-263987-ff6kor0c	170	1	However	however	RB
cord-263987-ff6kor0c	170	2	,	,	,
cord-263987-ff6kor0c	170	3	since	since	IN
cord-263987-ff6kor0c	170	4	these	these	DT
cord-263987-ff6kor0c	170	5	are	be	VBP
cord-263987-ff6kor0c	170	6	principled	principled	JJ
cord-263987-ff6kor0c	170	7	approximations	approximation	NNS
cord-263987-ff6kor0c	170	8	,	,	,
cord-263987-ff6kor0c	170	9	it	-PRON-	PRP
cord-263987-ff6kor0c	170	10	should	should	MD
cord-263987-ff6kor0c	170	11	be	be	VB
cord-263987-ff6kor0c	170	12	possible	possible	JJ
cord-263987-ff6kor0c	170	13	to	to	TO
cord-263987-ff6kor0c	170	14	form	form	VB
cord-263987-ff6kor0c	170	15	some	some	DT
cord-263987-ff6kor0c	170	16	conclusions	conclusion	NNS
cord-263987-ff6kor0c	170	17	as	as	IN
cord-263987-ff6kor0c	170	18	to	to	IN
cord-263987-ff6kor0c	170	19	the	the	DT
cord-263987-ff6kor0c	170	20	severity	severity	NN
cord-263987-ff6kor0c	170	21	of	of	IN
cord-263987-ff6kor0c	170	22	the	the	DT
cord-263987-ff6kor0c	170	23	error	error	NN
cord-263987-ff6kor0c	170	24	,	,	,
cord-263987-ff6kor0c	170	25	and	and	CC
cord-263987-ff6kor0c	170	26	its	-PRON-	PRP$
cord-263987-ff6kor0c	170	27	dependence	dependence	NN
cord-263987-ff6kor0c	170	28	on	on	IN
cord-263987-ff6kor0c	170	29	model	model	NN
cord-263987-ff6kor0c	170	30	parameters	parameter	NNS
cord-263987-ff6kor0c	170	31	.	.	.
cord-263987-ff6kor0c	171	1	Simulation	simulation	NN
cord-263987-ff6kor0c	171	2	studies	study	NNS
cord-263987-ff6kor0c	171	3	have	have	VBP
cord-263987-ff6kor0c	171	4	also	also	RB
cord-263987-ff6kor0c	171	5	been	be	VBN
cord-263987-ff6kor0c	171	6	of	of	IN
cord-263987-ff6kor0c	171	7	some	some	DT
cord-263987-ff6kor0c	171	8	help	help	NN
cord-263987-ff6kor0c	171	9	in	in	IN
cord-263987-ff6kor0c	171	10	assessing	assess	VBG
cord-263987-ff6kor0c	171	11	the	the	DT
cord-263987-ff6kor0c	171	12	error	error	NN
cord-263987-ff6kor0c	171	13	of	of	IN
cord-263987-ff6kor0c	171	14	these	these	DT
cord-263987-ff6kor0c	171	15	approximations	approximation	NNS
cord-263987-ff6kor0c	171	16	.	.	.
cord-263987-ff6kor0c	172	1	For	for	IN
cord-263987-ff6kor0c	172	2	context	context	NN
cord-263987-ff6kor0c	172	3	-	-	HYPH
cord-263987-ff6kor0c	172	4	dependent	dependent	JJ
cord-263987-ff6kor0c	172	5	substitution	substitution	NN
cord-263987-ff6kor0c	172	6	processes	process	NNS
cord-263987-ff6kor0c	172	7	,	,	,
cord-263987-ff6kor0c	172	8	such	such	JJ
cord-263987-ff6kor0c	172	9	as	as	IN
cord-263987-ff6kor0c	172	10	models	model	NNS
cord-263987-ff6kor0c	172	11	that	that	WDT
cord-263987-ff6kor0c	172	12	include	include	VBP
cord-263987-ff6kor0c	172	13	methylation	methylation	NN
cord-263987-ff6kor0c	172	14	-	-	HYPH
cord-263987-ff6kor0c	172	15	induced	induce	VBN
cord-263987-ff6kor0c	172	16	CpGdeamination	CpGdeamination	NNP
cord-263987-ff6kor0c	172	17	,	,	,
cord-263987-ff6kor0c	172	18	a	a	DT
cord-263987-ff6kor0c	172	19	clever	clever	JJ
cord-263987-ff6kor0c	172	20	approach	approach	NN
cord-263987-ff6kor0c	172	21	was	be	VBD
cord-263987-ff6kor0c	172	22	developed	develop	VBN
cord-263987-ff6kor0c	172	23	in	in	IN
cord-263987-ff6kor0c	172	24	[	[	-LRB-
cord-263987-ff6kor0c	172	25	44	44	CD
cord-263987-ff6kor0c	172	26	]	]	-RRB-
cord-263987-ff6kor0c	172	27	.	.	.
cord-263987-ff6kor0c	173	1	Rather	rather	RB
cord-263987-ff6kor0c	173	2	than	than	IN
cord-263987-ff6kor0c	173	3	considering	consider	VBG
cord-263987-ff6kor0c	173	4	a	a	DT
cord-263987-ff6kor0c	173	5	finite	finite	JJ
cord-263987-ff6kor0c	173	6	-	-	HYPH
cord-263987-ff6kor0c	173	7	event	event	NN
cord-263987-ff6kor0c	173	8	trajectory	trajectory	NN
cord-263987-ff6kor0c	173	9	,	,	,
cord-263987-ff6kor0c	173	10	they	-PRON-	PRP
cord-263987-ff6kor0c	173	11	develop	develop	VBP
cord-263987-ff6kor0c	173	12	an	an	DT
cord-263987-ff6kor0c	173	13	explicit	explicit	JJ
cord-263987-ff6kor0c	173	14	Taylor	Taylor	NNP
cord-263987-ff6kor0c	173	15	series	series	NN
cord-263987-ff6kor0c	173	16	for	for	IN
cord-263987-ff6kor0c	173	17	the	the	DT
cord-263987-ff6kor0c	173	18	matrix	matrix	NN
cord-263987-ff6kor0c	173	19	exponential	exponential	NN
cord-263987-ff6kor0c	173	20	(	(	-LRB-
cord-263987-ff6kor0c	173	21	Eq	Eq	NNP
cord-263987-ff6kor0c	173	22	.	.	NNP
cord-263987-ff6kor0c	173	23	2	2	LS
cord-263987-ff6kor0c	173	24	)	)	-RRB-
cord-263987-ff6kor0c	173	25	and	and	CC
cord-263987-ff6kor0c	173	26	then	then	RB
cord-263987-ff6kor0c	173	27	truncate	truncate	VB
cord-263987-ff6kor0c	173	28	this	this	DT
cord-263987-ff6kor0c	173	29	Taylor	Taylor	NNP
cord-263987-ff6kor0c	173	30	series	series	NN
cord-263987-ff6kor0c	173	31	.	.	.
cord-263987-ff6kor0c	174	1	Specifically	specifically	RB
cord-263987-ff6kor0c	174	2	,	,	,
cord-263987-ff6kor0c	174	3	the	the	DT
cord-263987-ff6kor0c	174	4	rate	rate	NN
cord-263987-ff6kor0c	174	5	matrix	matrix	NN
cord-263987-ff6kor0c	174	6	for	for	IN
cord-263987-ff6kor0c	174	7	a	a	DT
cord-263987-ff6kor0c	174	8	finite	finite	JJ
cord-263987-ff6kor0c	174	9	-	-	HYPH
cord-263987-ff6kor0c	174	10	length	length	NN
cord-263987-ff6kor0c	174	11	sequence	sequence	NN
cord-263987-ff6kor0c	174	12	is	be	VBZ
cord-263987-ff6kor0c	174	13	constructed	construct	VBN
cord-263987-ff6kor0c	174	14	as	as	IN
cord-263987-ff6kor0c	174	15	a	a	DT
cord-263987-ff6kor0c	174	16	sum	sum	NN
cord-263987-ff6kor0c	174	17	of	of	IN
cord-263987-ff6kor0c	174	18	rate	rate	NN
cord-263987-ff6kor0c	174	19	matrices	matrix	NNS
cord-263987-ff6kor0c	174	20	operating	operate	VBG
cord-263987-ff6kor0c	174	21	locally	locally	RB
cord-263987-ff6kor0c	174	22	on	on	IN
cord-263987-ff6kor0c	174	23	the	the	DT
cord-263987-ff6kor0c	174	24	sequence	sequence	NN
cord-263987-ff6kor0c	174	25	,	,	,
cord-263987-ff6kor0c	174	26	using	use	VBG
cord-263987-ff6kor0c	174	27	the	the	DT
cord-263987-ff6kor0c	174	28	Kronecker	Kronecker	NNP
cord-263987-ff6kor0c	174	29	sum	sum	NN
cord-263987-ff6kor0c	174	30	⊕	⊕	NNP
cord-263987-ff6kor0c	174	31	and	and	CC
cord-263987-ff6kor0c	174	32	Kronecker	Kronecker	NNP
cord-263987-ff6kor0c	174	33	product	product	NN
cord-263987-ff6kor0c	174	34	⊗	⊗	NN
cord-263987-ff6kor0c	174	35	to	to	TO
cord-263987-ff6kor0c	174	36	concatenate	concatenate	VB
cord-263987-ff6kor0c	174	37	rate	rate	NN
cord-263987-ff6kor0c	174	38	matrices	matrix	NNS
cord-263987-ff6kor0c	174	39	.	.	.
cord-263987-ff6kor0c	175	1	These	these	DT
cord-263987-ff6kor0c	175	2	operators	operator	NNS
cord-263987-ff6kor0c	175	3	may	may	MD
cord-263987-ff6kor0c	175	4	be	be	VB
cord-263987-ff6kor0c	175	5	understood	understand	VBN
cord-263987-ff6kor0c	175	6	as	as	IN
cord-263987-ff6kor0c	175	7	follows	follow	VBZ
cord-263987-ff6kor0c	175	8	,	,	,
cord-263987-ff6kor0c	175	9	for	for	IN
cord-263987-ff6kor0c	175	10	an	an	DT
cord-263987-ff6kor0c	175	11	alphabet	alphabet	NN
cord-263987-ff6kor0c	175	12	of	of	IN
cord-263987-ff6kor0c	175	13	N	n	CD
cord-263987-ff6kor0c	175	14	symbols	symbol	NNS
cord-263987-ff6kor0c	175	15	:	:	:
cord-263987-ff6kor0c	175	16	suppose	suppose	VB
cord-263987-ff6kor0c	175	17	that	that	IN
cord-263987-ff6kor0c	175	18	M	M	NNP
cord-263987-ff6kor0c	175	19	m	m	NNP
cord-263987-ff6kor0c	175	20	is	be	VBZ
cord-263987-ff6kor0c	175	21	the	the	DT
cord-263987-ff6kor0c	175	22	set	set	NN
cord-263987-ff6kor0c	175	23	of	of	IN
cord-263987-ff6kor0c	175	24	all	all	DT
cord-263987-ff6kor0c	175	25	matrices	matrix	NNS
cord-263987-ff6kor0c	175	26	indexed	index	VBN
cord-263987-ff6kor0c	175	27	by	by	IN
cord-263987-ff6kor0c	175	28	m	m	NNP
cord-263987-ff6kor0c	175	29	-	-	HYPH
cord-263987-ff6kor0c	175	30	mers	mers	NNPS
cord-263987-ff6kor0c	175	31	,	,	,
cord-263987-ff6kor0c	175	32	so	so	IN
cord-263987-ff6kor0c	175	33	that	that	IN
cord-263987-ff6kor0c	175	34	if	if	IN
cord-263987-ff6kor0c	175	35	A	a	DT
cord-263987-ff6kor0c	175	36	∈	∈	NN
cord-263987-ff6kor0c	175	37	M	M	NNP
cord-263987-ff6kor0c	175	38	m	m	NN
cord-263987-ff6kor0c	175	39	,	,	,
cord-263987-ff6kor0c	175	40	then	then	RB
cord-263987-ff6kor0c	175	41	A	a	DT
cord-263987-ff6kor0c	175	42	is	be	VBZ
cord-263987-ff6kor0c	175	43	an	an	DT
cord-263987-ff6kor0c	175	44	N	n	NN
cord-263987-ff6kor0c	175	45	m	m	NN
cord-263987-ff6kor0c	175	46	×	×	NN
cord-263987-ff6kor0c	175	47	N	n	NN
cord-263987-ff6kor0c	175	48	m	m	NN
cord-263987-ff6kor0c	175	49	matrix	matrix	NN
cord-263987-ff6kor0c	175	50	.	.	.
cord-263987-ff6kor0c	176	1	Let	let	VB
cord-263987-ff6kor0c	176	2	i	i	PRP
cord-263987-ff6kor0c	176	3	,	,	,
cord-263987-ff6kor0c	176	4	j	j	NNP
cord-263987-ff6kor0c	176	5	be	be	VB
cord-263987-ff6kor0c	176	6	m	m	NNP
cord-263987-ff6kor0c	176	7	-	-	HYPH
cord-263987-ff6kor0c	176	8	mers	mers	NNP
cord-263987-ff6kor0c	176	9	,	,	,
cord-263987-ff6kor0c	177	1	k	k	NNP
cord-263987-ff6kor0c	177	2	,	,	,
cord-263987-ff6kor0c	177	3	l	l	NNP
cord-263987-ff6kor0c	177	4	be	be	VB
cord-263987-ff6kor0c	177	5	n	n	NNP
cord-263987-ff6kor0c	177	6	-	-	HYPH
cord-263987-ff6kor0c	177	7	mers	mers	NNPS
cord-263987-ff6kor0c	177	8	,	,	,
cord-263987-ff6kor0c	177	9	and	and	CC
cord-263987-ff6kor0c	177	10	ik	ik	UH
cord-263987-ff6kor0c	177	11	,	,	,
cord-263987-ff6kor0c	177	12	jl	jl	NNP
cord-263987-ff6kor0c	177	13	the	the	DT
cord-263987-ff6kor0c	177	14	concatenated	concatenate	VBN
cord-263987-ff6kor0c	177	15	m	m	NNP
cord-263987-ff6kor0c	177	16	+	+	CC
cord-263987-ff6kor0c	177	17	n	n	NNP
cord-263987-ff6kor0c	177	18	-	-	HYPH
cord-263987-ff6kor0c	177	19	mers	mers	NNP
cord-263987-ff6kor0c	177	20	.	.	.
cord-263987-ff6kor0c	178	1	If	if	IN
cord-263987-ff6kor0c	178	2	A	a	DT
cord-263987-ff6kor0c	178	3	∈	∈	NN
cord-263987-ff6kor0c	178	4	M	m	NN
cord-263987-ff6kor0c	178	5	m	m	NN
cord-263987-ff6kor0c	178	6	and	and	CC
cord-263987-ff6kor0c	178	7	B	B	NNP
cord-263987-ff6kor0c	178	8	∈	∈	NN
cord-263987-ff6kor0c	178	9	M	m	NN
cord-263987-ff6kor0c	178	10	n	n	NN
cord-263987-ff6kor0c	178	11	then	then	RB
cord-263987-ff6kor0c	178	12	A	a	DT
cord-263987-ff6kor0c	178	13	⊕	⊕	NNP
cord-263987-ff6kor0c	178	14	B	B	NNP
cord-263987-ff6kor0c	178	15	and	and	CC
cord-263987-ff6kor0c	178	16	A	a	DT
cord-263987-ff6kor0c	178	17	⊗	⊗	NN
cord-263987-ff6kor0c	178	18	B	B	NNP
cord-263987-ff6kor0c	178	19	are	be	VBP
cord-263987-ff6kor0c	178	20	both	both	DT
cord-263987-ff6kor0c	178	21	in	in	IN
cord-263987-ff6kor0c	178	22	M	M	NNP
cord-263987-ff6kor0c	178	23	m+n	m+n	NNP
cord-263987-ff6kor0c	178	24	and	and	CC
cord-263987-ff6kor0c	178	25	are	be	VBP
cord-263987-ff6kor0c	178	26	specified	specify	VBN
cord-263987-ff6kor0c	178	27	by	by	IN
cord-263987-ff6kor0c	178	28	where	where	WRB
cord-263987-ff6kor0c	178	29	Commuting	commute	VBG
cord-263987-ff6kor0c	178	30	terms	term	NNS
cord-263987-ff6kor0c	178	31	in	in	IN
cord-263987-ff6kor0c	178	32	the	the	DT
cord-263987-ff6kor0c	178	33	Taylor	Taylor	NNP
cord-263987-ff6kor0c	178	34	series	series	NN
cord-263987-ff6kor0c	178	35	for	for	IN
cord-263987-ff6kor0c	178	36	exp(Rt	exp(Rt	NNP
cord-263987-ff6kor0c	178	37	)	)	-RRB-
cord-263987-ff6kor0c	178	38	can	can	MD
cord-263987-ff6kor0c	178	39	then	then	RB
cord-263987-ff6kor0c	178	40	be	be	VB
cord-263987-ff6kor0c	178	41	systematically	systematically	RB
cord-263987-ff6kor0c	178	42	rearranged	rearrange	VBN
cord-263987-ff6kor0c	178	43	into	into	IN
cord-263987-ff6kor0c	178	44	a	a	DT
cord-263987-ff6kor0c	178	45	quicklyconverging	quicklyconverge	VBG
cord-263987-ff6kor0c	178	46	dynamic	dynamic	JJ
cord-263987-ff6kor0c	178	47	programming	programming	NN
cord-263987-ff6kor0c	178	48	recursion	recursion	NN
cord-263987-ff6kor0c	178	49	.	.	.
cord-263987-ff6kor0c	179	1	This	this	DT
cord-263987-ff6kor0c	179	2	approach	approach	NN
cord-263987-ff6kor0c	179	3	was	be	VBD
cord-263987-ff6kor0c	179	4	first	first	RB
cord-263987-ff6kor0c	179	5	used	use	VBN
cord-263987-ff6kor0c	179	6	by	by	IN
cord-263987-ff6kor0c	179	7	[	[	-LRB-
cord-263987-ff6kor0c	179	8	44	44	CD
cord-263987-ff6kor0c	179	9	]	]	-RRB-
cord-263987-ff6kor0c	179	10	and	and	CC
cord-263987-ff6kor0c	179	11	further	further	RB
cord-263987-ff6kor0c	179	12	developed	develop	VBN
cord-263987-ff6kor0c	179	13	including	include	VBG
cord-263987-ff6kor0c	179	14	model	model	NN
cord-263987-ff6kor0c	179	15	-	-	HYPH
cord-263987-ff6kor0c	179	16	fitting	fit	VBG
cord-263987-ff6kor0c	179	17	algorithms	algorithm	NNS
cord-263987-ff6kor0c	179	18	[	[	-LRB-
cord-263987-ff6kor0c	179	19	86	86	CD
cord-263987-ff6kor0c	179	20	]	]	-RRB-
cord-263987-ff6kor0c	179	21	application	application	NN
cord-263987-ff6kor0c	179	22	to	to	TO
cord-263987-ff6kor0c	179	23	phylogenetic	phylogenetic	VB
cord-263987-ff6kor0c	179	24	trees	tree	NNS
cord-263987-ff6kor0c	179	25	[	[	-LRB-
cord-263987-ff6kor0c	179	26	87	87	CD
cord-263987-ff6kor0c	179	27	]	]	-RRB-
cord-263987-ff6kor0c	179	28	and	and	CC
cord-263987-ff6kor0c	179	29	discussion	discussion	NN
cord-263987-ff6kor0c	179	30	of	of	IN
cord-263987-ff6kor0c	179	31	the	the	DT
cord-263987-ff6kor0c	179	32	associated	associate	VBN
cord-263987-ff6kor0c	179	33	eigensystem	eigensystem	NNP
cord-263987-ff6kor0c	179	34	[	[	-LRB-
cord-263987-ff6kor0c	179	35	45	45	CD
cord-263987-ff6kor0c	179	36	,	,	,
cord-263987-ff6kor0c	179	37	62	62	CD
cord-263987-ff6kor0c	179	38	]	]	-RRB-
cord-263987-ff6kor0c	179	39	.	.	.
cord-263987-ff6kor0c	180	1	It	-PRON-	PRP
cord-263987-ff6kor0c	180	2	remains	remain	VBZ
cord-263987-ff6kor0c	180	3	to	to	TO
cord-263987-ff6kor0c	180	4	be	be	VB
cord-263987-ff6kor0c	180	5	seen	see	VBN
cord-263987-ff6kor0c	180	6	to	to	TO
cord-263987-ff6kor0c	180	7	what	what	WDT
cord-263987-ff6kor0c	180	8	extent	extent	NN
cord-263987-ff6kor0c	180	9	such	such	PDT
cord-263987-ff6kor0c	180	10	an	an	DT
cord-263987-ff6kor0c	180	11	approach	approach	NN
cord-263987-ff6kor0c	180	12	offers	offer	VBZ
cord-263987-ff6kor0c	180	13	a	a	DT
cord-263987-ff6kor0c	180	14	practical	practical	JJ
cord-263987-ff6kor0c	180	15	solution	solution	NN
cord-263987-ff6kor0c	180	16	for	for	IN
cord-263987-ff6kor0c	180	17	general	general	JJ
cord-263987-ff6kor0c	180	18	indel	indel	NNP
cord-263987-ff6kor0c	180	19	models	model	NNS
cord-263987-ff6kor0c	180	20	,	,	,
cord-263987-ff6kor0c	180	21	where	where	WRB
cord-263987-ff6kor0c	180	22	the	the	DT
cord-263987-ff6kor0c	180	23	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	180	24	transitions	transition	NNS
cord-263987-ff6kor0c	180	25	are	be	VBP
cord-263987-ff6kor0c	180	26	between	between	IN
cord-263987-ff6kor0c	180	27	sequences	sequence	NNS
cord-263987-ff6kor0c	180	28	of	of	IN
cord-263987-ff6kor0c	180	29	differing	differ	VBG
cord-263987-ff6kor0c	180	30	lengths	length	NNS
cord-263987-ff6kor0c	180	31	.	.	.
cord-263987-ff6kor0c	181	1	Such	such	JJ
cord-263987-ff6kor0c	181	2	is	be	VBZ
cord-263987-ff6kor0c	181	3	the	the	DT
cord-263987-ff6kor0c	181	4	difficulty	difficulty	NN
cord-263987-ff6kor0c	181	5	of	of	IN
cord-263987-ff6kor0c	181	6	solving	solve	VBG
cord-263987-ff6kor0c	181	7	long	long	JJ
cord-263987-ff6kor0c	181	8	indel	indel	NN
cord-263987-ff6kor0c	181	9	models	model	NNS
cord-263987-ff6kor0c	181	10	that	that	IN
cord-263987-ff6kor0c	181	11	several	several	JJ
cord-263987-ff6kor0c	181	12	authors	author	NNS
cord-263987-ff6kor0c	181	13	have	have	VBP
cord-263987-ff6kor0c	181	14	performed	perform	VBN
cord-263987-ff6kor0c	181	15	simulations	simulation	NNS
cord-263987-ff6kor0c	181	16	to	to	TO
cord-263987-ff6kor0c	181	17	investigate	investigate	VB
cord-263987-ff6kor0c	181	18	the	the	DT
cord-263987-ff6kor0c	181	19	empirical	empirical	JJ
cord-263987-ff6kor0c	181	20	gap	gap	NN
cord-263987-ff6kor0c	181	21	length	length	NN
cord-263987-ff6kor0c	181	22	distributions	distribution	NNS
cord-263987-ff6kor0c	181	23	that	that	WDT
cord-263987-ff6kor0c	181	24	are	be	VBP
cord-263987-ff6kor0c	181	25	observed	observe	VBN
cord-263987-ff6kor0c	181	26	after	after	IN
cord-263987-ff6kor0c	181	27	finite	finite	JJ
cord-263987-ff6kor0c	181	28	time	time	NN
cord-263987-ff6kor0c	181	29	intervals	interval	NNS
cord-263987-ff6kor0c	181	30	for	for	IN
cord-263987-ff6kor0c	181	31	various	various	JJ
cord-263987-ff6kor0c	181	32	given	give	VBN
cord-263987-ff6kor0c	181	33	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	181	34	indelrate	indelrate	JJ
cord-263987-ff6kor0c	181	35	models	model	NNS
cord-263987-ff6kor0c	181	36	.	.	.
cord-263987-ff6kor0c	182	1	These	these	DT
cord-263987-ff6kor0c	182	2	observed	observe	VBN
cord-263987-ff6kor0c	182	3	gaps	gap	NNS
cord-263987-ff6kor0c	182	4	can	can	MD
cord-263987-ff6kor0c	182	5	arise	arise	VB
cord-263987-ff6kor0c	182	6	from	from	IN
cord-263987-ff6kor0c	182	7	multiple	multiple	JJ
cord-263987-ff6kor0c	182	8	overlapping	overlapping	JJ
cord-263987-ff6kor0c	182	9	indel	indel	NN
cord-263987-ff6kor0c	182	10	events	event	NNS
cord-263987-ff6kor0c	182	11	,	,	,
cord-263987-ff6kor0c	182	12	in	in	IN
cord-263987-ff6kor0c	182	13	ways	way	NNS
cord-263987-ff6kor0c	182	14	that	that	WDT
cord-263987-ff6kor0c	182	15	have	have	VBP
cord-263987-ff6kor0c	182	16	so	so	RB
cord-263987-ff6kor0c	182	17	far	far	RB
cord-263987-ff6kor0c	182	18	defied	defy	VBN
cord-263987-ff6kor0c	182	19	straightforward	straightforward	JJ
cord-263987-ff6kor0c	182	20	algebraic	algebraic	JJ
cord-263987-ff6kor0c	182	21	characterization	characterization	NN
cord-263987-ff6kor0c	182	22	.	.	.
cord-263987-ff6kor0c	183	1	In	in	IN
cord-263987-ff6kor0c	183	2	recent	recent	JJ
cord-263987-ff6kor0c	183	3	work	work	NN
cord-263987-ff6kor0c	183	4	,	,	,
cord-263987-ff6kor0c	183	5	Rivas	Rivas	NNP
cord-263987-ff6kor0c	183	6	and	and	CC
cord-263987-ff6kor0c	183	7	Eddy	Eddy	NNP
cord-263987-ff6kor0c	183	8	[	[	-LRB-
cord-263987-ff6kor0c	183	9	56	56	CD
cord-263987-ff6kor0c	183	10	]	]	-RRB-
cord-263987-ff6kor0c	183	11	have	have	VBP
cord-263987-ff6kor0c	183	12	shown	show	VBN
cord-263987-ff6kor0c	183	13	that	that	IN
cord-263987-ff6kor0c	183	14	if	if	IN
cord-263987-ff6kor0c	183	15	an	an	DT
cord-263987-ff6kor0c	183	16	underlying	underlying	JJ
cord-263987-ff6kor0c	183	17	model	model	NN
cord-263987-ff6kor0c	183	18	has	have	VBZ
cord-263987-ff6kor0c	183	19	a	a	DT
cord-263987-ff6kor0c	183	20	simple	simple	JJ
cord-263987-ff6kor0c	183	21	geometric	geometric	JJ
cord-263987-ff6kor0c	183	22	length	length	NN
cord-263987-ff6kor0c	183	23	distribution	distribution	NN
cord-263987-ff6kor0c	183	24	over	over	IN
cord-263987-ff6kor0c	183	25	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	183	26	indel	indel	NN
cord-263987-ff6kor0c	183	27	events	event	NNS
cord-263987-ff6kor0c	183	28	,	,	,
cord-263987-ff6kor0c	183	29	the	the	DT
cord-263987-ff6kor0c	183	30	observed	observed	JJ
cord-263987-ff6kor0c	183	31	gap	gap	NN
cord-263987-ff6kor0c	183	32	length	length	NN
cord-263987-ff6kor0c	183	33	distribution	distribution	NN
cord-263987-ff6kor0c	183	34	at	at	IN
cord-263987-ff6kor0c	183	35	finite	finite	JJ
cord-263987-ff6kor0c	183	36	times	time	NNS
cord-263987-ff6kor0c	183	37	(	(	-LRB-
cord-263987-ff6kor0c	183	38	accounting	account	VBG
cord-263987-ff6kor0c	183	39	for	for	IN
cord-263987-ff6kor0c	183	40	the	the	DT
cord-263987-ff6kor0c	183	41	possibility	possibility	NN
cord-263987-ff6kor0c	183	42	of	of	IN
cord-263987-ff6kor0c	183	43	multiple	multiple	JJ
cord-263987-ff6kor0c	183	44	,	,	,
cord-263987-ff6kor0c	183	45	overlapping	overlap	VBG
cord-263987-ff6kor0c	183	46	indels	indel	NNS
cord-263987-ff6kor0c	183	47	)	)	-RRB-
cord-263987-ff6kor0c	183	48	can	can	MD
cord-263987-ff6kor0c	183	49	not	not	RB
cord-263987-ff6kor0c	183	50	be	be	VB
cord-263987-ff6kor0c	183	51	geometric	geometric	JJ
cord-263987-ff6kor0c	183	52	.	.	.
cord-263987-ff6kor0c	184	1	Rivas	Rivas	NNP
cord-263987-ff6kor0c	184	2	and	and	CC
cord-263987-ff6kor0c	184	3	Eddy	Eddy	NNP
cord-263987-ff6kor0c	184	4	report	report	NN
cord-263987-ff6kor0c	184	5	simulation	simulation	NN
cord-263987-ff6kor0c	184	6	studies	study	NNS
cord-263987-ff6kor0c	184	7	supporting	support	VBG
cord-263987-ff6kor0c	184	8	this	this	DT
cord-263987-ff6kor0c	184	9	result	result	NN
cord-263987-ff6kor0c	184	10	,	,	,
cord-263987-ff6kor0c	184	11	and	and	CC
cord-263987-ff6kor0c	184	12	go	go	VB
cord-263987-ff6kor0c	184	13	on	on	RP
cord-263987-ff6kor0c	184	14	to	to	TO
cord-263987-ff6kor0c	184	15	propose	propose	VB
cord-263987-ff6kor0c	184	16	several	several	JJ
cord-263987-ff6kor0c	184	17	models	model	NNS
cord-263987-ff6kor0c	184	18	incorporating	incorporate	VBG
cord-263987-ff6kor0c	184	19	hidden	hide	VBN
cord-263987-ff6kor0c	184	20	information	information	NN
cord-263987-ff6kor0c	184	21	(	(	-LRB-
cord-263987-ff6kor0c	184	22	such	such	JJ
cord-263987-ff6kor0c	184	23	as	as	IN
cord-263987-ff6kor0c	184	24	fragment	fragment	NN
cord-263987-ff6kor0c	184	25	boundaries	boundary	NNS
cord-263987-ff6kor0c	184	26	,	,	,
cord-263987-ff6kor0c	184	27	a	a	FW
cord-263987-ff6kor0c	184	28	la	la	FW
cord-263987-ff6kor0c	184	29	TKF92	TKF92	NNP
cord-263987-ff6kor0c	184	30	)	)	-RRB-
cord-263987-ff6kor0c	184	31	which	which	WDT
cord-263987-ff6kor0c	184	32	have	have	VBP
cord-263987-ff6kor0c	184	33	the	the	DT
cord-263987-ff6kor0c	184	34	advantage	advantage	NN
cord-263987-ff6kor0c	184	35	of	of	IN
cord-263987-ff6kor0c	184	36	being	be	VBG
cord-263987-ff6kor0c	184	37	good	good	JJ
cord-263987-ff6kor0c	184	38	fits	fit	NNS
cord-263987-ff6kor0c	184	39	to	to	IN
cord-263987-ff6kor0c	184	40	HMMs	HMMs	NNP
cord-263987-ff6kor0c	184	41	for	for	IN
cord-263987-ff6kor0c	184	42	their	-PRON-	PRP$
cord-263987-ff6kor0c	184	43	finite	finite	JJ
cord-263987-ff6kor0c	184	44	-	-	HYPH
cord-263987-ff6kor0c	184	45	time	time	NN
cord-263987-ff6kor0c	184	46	distributions	distribution	NNS
cord-263987-ff6kor0c	184	47	.	.	.
cord-263987-ff6kor0c	185	1	It	-PRON-	PRP
cord-263987-ff6kor0c	185	2	has	have	VBZ
cord-263987-ff6kor0c	185	3	long	long	RB
cord-263987-ff6kor0c	185	4	been	be	VBN
cord-263987-ff6kor0c	185	5	known	know	VBN
cord-263987-ff6kor0c	185	6	that	that	IN
cord-263987-ff6kor0c	185	7	the	the	DT
cord-263987-ff6kor0c	185	8	lengths	length	NNS
cord-263987-ff6kor0c	185	9	of	of	IN
cord-263987-ff6kor0c	185	10	empiricallyobserved	empiricallyobserved	JJ
cord-263987-ff6kor0c	185	11	indels	indel	NNS
cord-263987-ff6kor0c	185	12	are	be	VBP
cord-263987-ff6kor0c	185	13	more	more	RBR
cord-263987-ff6kor0c	185	14	accurately	accurately	RB
cord-263987-ff6kor0c	185	15	described	describe	VBN
cord-263987-ff6kor0c	185	16	by	by	IN
cord-263987-ff6kor0c	185	17	a	a	DT
cord-263987-ff6kor0c	185	18	power	power	NN
cord-263987-ff6kor0c	185	19	-	-	HYPH
cord-263987-ff6kor0c	185	20	law	law	NN
cord-263987-ff6kor0c	185	21	distribution	distribution	NN
cord-263987-ff6kor0c	185	22	than	than	IN
cord-263987-ff6kor0c	185	23	a	a	DT
cord-263987-ff6kor0c	185	24	geometric	geometric	JJ
cord-263987-ff6kor0c	185	25	distribution	distribution	NN
cord-263987-ff6kor0c	185	26	[	[	-LRB-
cord-263987-ff6kor0c	185	27	46	46	CD
cord-263987-ff6kor0c	185	28	,	,	,
cord-263987-ff6kor0c	185	29	47	47	CD
cord-263987-ff6kor0c	185	30	,	,	,
cord-263987-ff6kor0c	185	31	[	[	-LRB-
cord-263987-ff6kor0c	185	32	88	88	CD
cord-263987-ff6kor0c	185	33	]	]	-RRB-
cord-263987-ff6kor0c	185	34	[	[	-LRB-
cord-263987-ff6kor0c	185	35	89	89	CD
cord-263987-ff6kor0c	185	36	]	]	-RRB-
cord-263987-ff6kor0c	185	37	[	[	-LRB-
cord-263987-ff6kor0c	185	38	90	90	CD
cord-263987-ff6kor0c	185	39	]	]	-RRB-
cord-263987-ff6kor0c	185	40	[	[	-LRB-
cord-263987-ff6kor0c	185	41	91	91	CD
cord-263987-ff6kor0c	185	42	]	]	-RRB-
cord-263987-ff6kor0c	185	43	and	and	CC
cord-263987-ff6kor0c	185	44	that	that	IN
cord-263987-ff6kor0c	185	45	alignment	alignment	NN
cord-263987-ff6kor0c	185	46	algorithms	algorithm	NNS
cord-263987-ff6kor0c	185	47	may	may	MD
cord-263987-ff6kor0c	185	48	benefit	benefit	VB
cord-263987-ff6kor0c	185	49	from	from	IN
cord-263987-ff6kor0c	185	50	using	use	VBG
cord-263987-ff6kor0c	185	51	such	such	JJ
cord-263987-ff6kor0c	185	52	length	length	NN
cord-263987-ff6kor0c	185	53	distributions	distribution	NNS
cord-263987-ff6kor0c	185	54	,	,	,
cord-263987-ff6kor0c	185	55	which	which	WDT
cord-263987-ff6kor0c	185	56	lead	lead	VBP
cord-263987-ff6kor0c	185	57	to	to	IN
cord-263987-ff6kor0c	185	58	generalized	generalized	JJ
cord-263987-ff6kor0c	185	59	convex	convex	JJ
cord-263987-ff6kor0c	185	60	gap	gap	NN
cord-263987-ff6kor0c	185	61	penalties	penalty	NNS
cord-263987-ff6kor0c	185	62	,	,	,
cord-263987-ff6kor0c	185	63	rather	rather	RB
cord-263987-ff6kor0c	185	64	than	than	IN
cord-263987-ff6kor0c	185	65	the	the	DT
cord-263987-ff6kor0c	185	66	computationally	computationally	RB
cord-263987-ff6kor0c	185	67	more	more	RBR
cord-263987-ff6kor0c	185	68	convenient	convenient	JJ
cord-263987-ff6kor0c	185	69	geometric	geometric	JJ
cord-263987-ff6kor0c	185	70	distribution	distribution	NN
cord-263987-ff6kor0c	185	71	,	,	,
cord-263987-ff6kor0c	185	72	which	which	WDT
cord-263987-ff6kor0c	185	73	leads	lead	VBZ
cord-263987-ff6kor0c	185	74	to	to	IN
cord-263987-ff6kor0c	185	75	an	an	DT
cord-263987-ff6kor0c	185	76	affine	affine	JJ
cord-263987-ff6kor0c	185	77	or	or	CC
cord-263987-ff6kor0c	185	78	linear	linear	JJ
cord-263987-ff6kor0c	185	79	gap	gap	NN
cord-263987-ff6kor0c	185	80	penalty	penalty	NN
cord-263987-ff6kor0c	185	81	[	[	-LRB-
cord-263987-ff6kor0c	185	82	92	92	CD
cord-263987-ff6kor0c	185	83	,	,	,
cord-263987-ff6kor0c	185	84	93	93	CD
cord-263987-ff6kor0c	185	85	]	]	-RRB-
cord-263987-ff6kor0c	185	86	.	.	.
cord-263987-ff6kor0c	186	1	For	for	IN
cord-263987-ff6kor0c	186	2	molecular	molecular	JJ
cord-263987-ff6kor0c	186	3	evolution	evolution	NN
cord-263987-ff6kor0c	186	4	purposes	purpose	NNS
cord-263987-ff6kor0c	186	5	in	in	IN
cord-263987-ff6kor0c	186	6	particular	particular	JJ
cord-263987-ff6kor0c	186	7	,	,	,
cord-263987-ff6kor0c	186	8	it	-PRON-	PRP
cord-263987-ff6kor0c	186	9	is	be	VBZ
cord-263987-ff6kor0c	186	10	known	know	VBN
cord-263987-ff6kor0c	186	11	that	that	IN
cord-263987-ff6kor0c	186	12	overreliance	overreliance	NN
cord-263987-ff6kor0c	186	13	on	on	IN
cord-263987-ff6kor0c	186	14	affine	affine	JJ
cord-263987-ff6kor0c	186	15	gap	gap	NN
cord-263987-ff6kor0c	186	16	penalties	penalty	NNS
cord-263987-ff6kor0c	186	17	leads	lead	VBZ
cord-263987-ff6kor0c	186	18	to	to	IN
cord-263987-ff6kor0c	186	19	serious	serious	JJ
cord-263987-ff6kor0c	186	20	underestimates	underestimate	NNS
cord-263987-ff6kor0c	186	21	of	of	IN
cord-263987-ff6kor0c	186	22	the	the	DT
cord-263987-ff6kor0c	186	23	true	true	JJ
cord-263987-ff6kor0c	186	24	lengths	length	NNS
cord-263987-ff6kor0c	186	25	of	of	IN
cord-263987-ff6kor0c	186	26	natural	natural	JJ
cord-263987-ff6kor0c	186	27	indels	indel	NNS
cord-263987-ff6kor0c	186	28	[	[	-LRB-
cord-263987-ff6kor0c	186	29	94	94	CD
cord-263987-ff6kor0c	186	30	]	]	-RRB-
cord-263987-ff6kor0c	186	31	.	.	.
cord-263987-ff6kor0c	187	1	For	for	IN
cord-263987-ff6kor0c	187	2	almost	almost	RB
cord-263987-ff6kor0c	187	3	as	as	RB
cord-263987-ff6kor0c	187	4	long	long	JJ
cord-263987-ff6kor0c	187	5	,	,	,
cord-263987-ff6kor0c	187	6	it	-PRON-	PRP
cord-263987-ff6kor0c	187	7	has	have	VBZ
cord-263987-ff6kor0c	187	8	been	be	VBN
cord-263987-ff6kor0c	187	9	known	know	VBN
cord-263987-ff6kor0c	187	10	that	that	IN
cord-263987-ff6kor0c	187	11	using	use	VBG
cord-263987-ff6kor0c	187	12	a	a	DT
cord-263987-ff6kor0c	187	13	mixture	mixture	NN
cord-263987-ff6kor0c	187	14	of	of	IN
cord-263987-ff6kor0c	187	15	geometric	geometric	JJ
cord-263987-ff6kor0c	187	16	distributions	distribution	NNS
cord-263987-ff6kor0c	187	17	,	,	,
cord-263987-ff6kor0c	187	18	or	or	CC
cord-263987-ff6kor0c	187	19	(	(	-LRB-
cord-263987-ff6kor0c	187	20	considered	consider	VBN
cord-263987-ff6kor0c	187	21	in	in	IN
cord-263987-ff6kor0c	187	22	score	score	NN
cord-263987-ff6kor0c	187	23	space	space	NN
cord-263987-ff6kor0c	187	24	rather	rather	RB
cord-263987-ff6kor0c	187	25	than	than	IN
cord-263987-ff6kor0c	187	26	probability	probability	NN
cord-263987-ff6kor0c	187	27	space	space	NN
cord-263987-ff6kor0c	187	28	)	)	-RRB-
cord-263987-ff6kor0c	187	29	a	a	DT
cord-263987-ff6kor0c	187	30	piecewise	piecewise	JJ
cord-263987-ff6kor0c	187	31	linear	linear	JJ
cord-263987-ff6kor0c	187	32	gap	gap	NN
cord-263987-ff6kor0c	187	33	penalty	penalty	NN
cord-263987-ff6kor0c	187	34	,	,	,
cord-263987-ff6kor0c	187	35	mitigates	mitigate	VBZ
cord-263987-ff6kor0c	187	36	some	some	DT
cord-263987-ff6kor0c	187	37	of	of	IN
cord-263987-ff6kor0c	187	38	these	these	DT
cord-263987-ff6kor0c	187	39	problems	problem	NNS
cord-263987-ff6kor0c	187	40	in	in	IN
cord-263987-ff6kor0c	187	41	sequence	sequence	NN
cord-263987-ff6kor0c	187	42	alignment	alignment	NN
cord-263987-ff6kor0c	187	43	[	[	-LRB-
cord-263987-ff6kor0c	187	44	94	94	CD
cord-263987-ff6kor0c	187	45	]	]	-RRB-
cord-263987-ff6kor0c	187	46	[	[	-LRB-
cord-263987-ff6kor0c	187	47	95	95	CD
cord-263987-ff6kor0c	187	48	]	]	-RRB-
cord-263987-ff6kor0c	187	49	[	[	-LRB-
cord-263987-ff6kor0c	187	50	96	96	CD
cord-263987-ff6kor0c	187	51	]	]	-RRB-
cord-263987-ff6kor0c	187	52	.	.	.
cord-263987-ff6kor0c	188	1	Taken	take	VBN
cord-263987-ff6kor0c	188	2	together	together	RB
cord-263987-ff6kor0c	188	3	,	,	,
cord-263987-ff6kor0c	188	4	these	these	DT
cord-263987-ff6kor0c	188	5	results	result	NNS
cord-263987-ff6kor0c	188	6	suggest	suggest	VBP
cord-263987-ff6kor0c	188	7	that	that	IN
cord-263987-ff6kor0c	188	8	simple	simple	JJ
cord-263987-ff6kor0c	188	9	HMM	hmm	NN
cord-263987-ff6kor0c	188	10	-	-	HYPH
cord-263987-ff6kor0c	188	11	like	like	JJ
cord-263987-ff6kor0c	188	12	models	model	NNS
cord-263987-ff6kor0c	188	13	,	,	,
cord-263987-ff6kor0c	188	14	which	which	WDT
cord-263987-ff6kor0c	188	15	are	be	VBP
cord-263987-ff6kor0c	188	16	most	most	RBS
cord-263987-ff6kor0c	188	17	efficient	efficient	JJ
cord-263987-ff6kor0c	188	18	at	at	IN
cord-263987-ff6kor0c	188	19	modeling	model	VBG
cord-263987-ff6kor0c	188	20	geometric	geometric	JJ
cord-263987-ff6kor0c	188	21	length	length	NN
cord-263987-ff6kor0c	188	22	distributions	distribution	NNS
cord-263987-ff6kor0c	188	23	,	,	,
cord-263987-ff6kor0c	188	24	may	may	MD
cord-263987-ff6kor0c	188	25	be	be	VB
cord-263987-ff6kor0c	188	26	fundamentally	fundamentally	RB
cord-263987-ff6kor0c	188	27	limited	limit	VBN
cord-263987-ff6kor0c	188	28	in	in	IN
cord-263987-ff6kor0c	188	29	their	-PRON-	PRP$
cord-263987-ff6kor0c	188	30	ability	ability	NN
cord-263987-ff6kor0c	188	31	to	to	TO
cord-263987-ff6kor0c	188	32	fully	fully	RB
cord-263987-ff6kor0c	188	33	describe	describe	VB
cord-263987-ff6kor0c	188	34	indels	indel	NNS
cord-263987-ff6kor0c	188	35	;	;	:
cord-263987-ff6kor0c	188	36	that	that	IN
cord-263987-ff6kor0c	188	37	adding	add	VBG
cord-263987-ff6kor0c	188	38	more	more	JJR
cord-263987-ff6kor0c	188	39	states	state	NNS
cord-263987-ff6kor0c	188	40	(	(	-LRB-
cord-263987-ff6kor0c	188	41	yielding	yield	VBG
cord-263987-ff6kor0c	188	42	length	length	NN
cord-263987-ff6kor0c	188	43	distributions	distribution	NNS
cord-263987-ff6kor0c	188	44	that	that	WDT
cord-263987-ff6kor0c	188	45	arise	arise	VBP
cord-263987-ff6kor0c	188	46	from	from	IN
cord-263987-ff6kor0c	188	47	sums	sum	NNS
cord-263987-ff6kor0c	188	48	of	of	IN
cord-263987-ff6kor0c	188	49	geometric	geometric	JJ
cord-263987-ff6kor0c	188	50	random	random	JJ
cord-263987-ff6kor0c	188	51	variates	variate	NNS
cord-263987-ff6kor0c	188	52	,	,	,
cord-263987-ff6kor0c	188	53	such	such	JJ
cord-263987-ff6kor0c	188	54	as	as	IN
cord-263987-ff6kor0c	188	55	negative	negative	JJ
cord-263987-ff6kor0c	188	56	binomial	binomial	JJ
cord-263987-ff6kor0c	188	57	distributions	distribution	NNS
cord-263987-ff6kor0c	188	58	,	,	,
cord-263987-ff6kor0c	188	59	or	or	CC
cord-263987-ff6kor0c	188	60	mixtures	mixture	NNS
cord-263987-ff6kor0c	188	61	of	of	IN
cord-263987-ff6kor0c	188	62	geometric	geometric	JJ
cord-263987-ff6kor0c	188	63	distributions	distribution	NNS
cord-263987-ff6kor0c	188	64	)	)	-RRB-
cord-263987-ff6kor0c	188	65	can	can	MD
cord-263987-ff6kor0c	188	66	lead	lead	VB
cord-263987-ff6kor0c	188	67	to	to	IN
cord-263987-ff6kor0c	188	68	an	an	DT
cord-263987-ff6kor0c	188	69	improvement	improvement	NN
cord-263987-ff6kor0c	188	70	;	;	:
cord-263987-ff6kor0c	188	71	and	and	CC
cord-263987-ff6kor0c	188	72	that	that	IN
cord-263987-ff6kor0c	188	73	generalized	generalized	JJ
cord-263987-ff6kor0c	188	74	HMMs	HMMs	NNP
cord-263987-ff6kor0c	188	75	,	,	,
cord-263987-ff6kor0c	188	76	which	which	WDT
cord-263987-ff6kor0c	188	77	can	can	MD
cord-263987-ff6kor0c	188	78	model	model	VB
cord-263987-ff6kor0c	188	79	arbitrary	arbitrary	JJ
cord-263987-ff6kor0c	188	80	length	length	NN
cord-263987-ff6kor0c	188	81	distributions	distribution	NNS
cord-263987-ff6kor0c	188	82	at	at	IN
cord-263987-ff6kor0c	188	83	the	the	DT
cord-263987-ff6kor0c	188	84	cost	cost	NN
cord-263987-ff6kor0c	188	85	of	of	IN
cord-263987-ff6kor0c	188	86	some	some	DT
cord-263987-ff6kor0c	188	87	computational	computational	JJ
cord-263987-ff6kor0c	188	88	efficiency	efficiency	NN
cord-263987-ff6kor0c	188	89	[	[	-LRB-
cord-263987-ff6kor0c	188	90	97	97	CD
cord-263987-ff6kor0c	188	91	]	]	-RRB-
cord-263987-ff6kor0c	188	92	,	,	,
cord-263987-ff6kor0c	188	93	may	may	MD
cord-263987-ff6kor0c	188	94	be	be	VB
cord-263987-ff6kor0c	188	95	most	most	RBS
cord-263987-ff6kor0c	188	96	appropriate	appropriate	JJ
cord-263987-ff6kor0c	188	97	.	.	.
cord-263987-ff6kor0c	189	1	For	for	IN
cord-263987-ff6kor0c	189	2	example	example	NN
cord-263987-ff6kor0c	189	3	,	,	,
cord-263987-ff6kor0c	189	4	the	the	DT
cord-263987-ff6kor0c	189	5	abovementioned	abovementioned	JJ
cord-263987-ff6kor0c	189	6	"	"	``
cord-263987-ff6kor0c	189	7	long	long	JJ
cord-263987-ff6kor0c	189	8	indel	indel	NN
cord-263987-ff6kor0c	189	9	"	"	''
cord-263987-ff6kor0c	189	10	model	model	NN
cord-263987-ff6kor0c	189	11	of	of	IN
cord-263987-ff6kor0c	189	12	Miklós	Miklós	NNP
cord-263987-ff6kor0c	189	13	et	et	NNP
cord-263987-ff6kor0c	189	14	al	al	NNP
cord-263987-ff6kor0c	189	15	.	.	NNP
cord-263987-ff6kor0c	189	16	uses	use	VBZ
cord-263987-ff6kor0c	189	17	a	a	DT
cord-263987-ff6kor0c	189	18	generalized	generalized	JJ
cord-263987-ff6kor0c	189	19	Pair	pair	NN
cord-263987-ff6kor0c	189	20	HMM	hmm	NN
cord-263987-ff6kor0c	189	21	[	[	-LRB-
cord-263987-ff6kor0c	189	22	84	84	CD
cord-263987-ff6kor0c	189	23	]	]	-RRB-
cord-263987-ff6kor0c	189	24	,	,	,
cord-263987-ff6kor0c	189	25	as	as	IN
cord-263987-ff6kor0c	189	26	does	do	VBZ
cord-263987-ff6kor0c	189	27	the	the	DT
cord-263987-ff6kor0c	189	28	HMM	HMM	NNP
cord-263987-ff6kor0c	189	29	of	of	IN
cord-263987-ff6kor0c	189	30	[	[	-LRB-
cord-263987-ff6kor0c	189	31	98	98	CD
cord-263987-ff6kor0c	189	32	]	]	-RRB-
cord-263987-ff6kor0c	189	33	.	.	.
cord-263987-ff6kor0c	190	1	It	-PRON-	PRP
cord-263987-ff6kor0c	190	2	is	be	VBZ
cord-263987-ff6kor0c	190	3	even	even	RB
cord-263987-ff6kor0c	190	4	conceivable	conceivable	JJ
cord-263987-ff6kor0c	190	5	that	that	IN
cord-263987-ff6kor0c	190	6	some	some	DT
cord-263987-ff6kor0c	190	7	molecular	molecular	JJ
cord-263987-ff6kor0c	190	8	evolution	evolution	NN
cord-263987-ff6kor0c	190	9	studies	study	NNS
cord-263987-ff6kor0c	190	10	in	in	IN
cord-263987-ff6kor0c	190	11	the	the	DT
cord-263987-ff6kor0c	190	12	future	future	NN
cord-263987-ff6kor0c	190	13	will	will	MD
cord-263987-ff6kor0c	190	14	abandon	abandon	VB
cord-263987-ff6kor0c	190	15	HMMs	HMMs	NNP
cord-263987-ff6kor0c	190	16	altogether	altogether	RB
cord-263987-ff6kor0c	190	17	,	,	,
cord-263987-ff6kor0c	190	18	although	although	IN
cord-263987-ff6kor0c	190	19	they	-PRON-	PRP
cord-263987-ff6kor0c	190	20	remain	remain	VBP
cord-263987-ff6kor0c	190	21	very	very	RB
cord-263987-ff6kor0c	190	22	convenient	convenient	JJ
cord-263987-ff6kor0c	190	23	for	for	IN
cord-263987-ff6kor0c	190	24	many	many	JJ
cord-263987-ff6kor0c	190	25	applications	application	NNS
cord-263987-ff6kor0c	190	26	.	.	.
cord-263987-ff6kor0c	191	1	The	the	DT
cord-263987-ff6kor0c	191	2	recent	recent	JJ
cord-263987-ff6kor0c	191	3	work	work	NN
cord-263987-ff6kor0c	191	4	of	of	IN
cord-263987-ff6kor0c	191	5	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	191	6	has	have	VBZ
cord-263987-ff6kor0c	191	7	some	some	DT
cord-263987-ff6kor0c	191	8	parallels	parallel	NNS
cord-263987-ff6kor0c	191	9	,	,	,
cord-263987-ff6kor0c	191	10	but	but	CC
cord-263987-ff6kor0c	191	11	also	also	RB
cord-263987-ff6kor0c	191	12	differences	difference	NNS
cord-263987-ff6kor0c	191	13	,	,	,
cord-263987-ff6kor0c	191	14	to	to	IN
cord-263987-ff6kor0c	191	15	the	the	DT
cord-263987-ff6kor0c	191	16	work	work	NN
cord-263987-ff6kor0c	191	17	of	of	IN
cord-263987-ff6kor0c	191	18	Rivas	Rivas	NNP
cord-263987-ff6kor0c	191	19	and	and	CC
cord-263987-ff6kor0c	191	20	Eddy	Eddy	NNP
cord-263987-ff6kor0c	191	21	[	[	-LRB-
cord-263987-ff6kor0c	191	22	53	53	CD
cord-263987-ff6kor0c	191	23	]	]	-RRB-
cord-263987-ff6kor0c	191	24	[	[	-LRB-
cord-263987-ff6kor0c	191	25	54	54	CD
cord-263987-ff6kor0c	191	26	]	]	-RRB-
cord-263987-ff6kor0c	191	27	[	[	-LRB-
cord-263987-ff6kor0c	191	28	55	55	CD
cord-263987-ff6kor0c	191	29	]	]	-RRB-
cord-263987-ff6kor0c	191	30	.	.	.
cord-263987-ff6kor0c	192	1	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	192	2	criticizes	criticize	VBZ
cord-263987-ff6kor0c	192	3	over	over	IN
cord-263987-ff6kor0c	192	4	-	-	HYPH
cord-263987-ff6kor0c	192	5	reliance	reliance	NN
cord-263987-ff6kor0c	192	6	on	on	IN
cord-263987-ff6kor0c	192	7	HMM	HMM	NNP
cord-263987-ff6kor0c	192	8	-	-	HYPH
cord-263987-ff6kor0c	192	9	like	like	JJ
cord-263987-ff6kor0c	192	10	models	model	NNS
cord-263987-ff6kor0c	192	11	,	,	,
cord-263987-ff6kor0c	192	12	and	and	CC
cord-263987-ff6kor0c	192	13	insists	insist	VBZ
cord-263987-ff6kor0c	192	14	on	on	IN
cord-263987-ff6kor0c	192	15	a	a	DT
cord-263987-ff6kor0c	192	16	systematic	systematic	JJ
cord-263987-ff6kor0c	192	17	derivation	derivation	NN
cord-263987-ff6kor0c	192	18	from	from	IN
cord-263987-ff6kor0c	192	19	simple	simple	JJ
cord-263987-ff6kor0c	192	20	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	192	21	models	model	NNS
cord-263987-ff6kor0c	192	22	.	.	.
cord-263987-ff6kor0c	193	1	He	-PRON-	PRP
cord-263987-ff6kor0c	193	2	puts	put	VBZ
cord-263987-ff6kor0c	193	3	the	the	DT
cord-263987-ff6kor0c	193	4	intuition	intuition	NN
cord-263987-ff6kor0c	193	5	of	of	IN
cord-263987-ff6kor0c	193	6	Miklós	Miklós	NNP
cord-263987-ff6kor0c	193	7	et	et	NNP
cord-263987-ff6kor0c	193	8	al	al	NNP
cord-263987-ff6kor0c	193	9	[	[	-LRB-
cord-263987-ff6kor0c	193	10	84	84	CD
cord-263987-ff6kor0c	193	11	]	]	-RRB-
cord-263987-ff6kor0c	193	12	on	on	IN
cord-263987-ff6kor0c	193	13	a	a	DT
cord-263987-ff6kor0c	193	14	more	more	RBR
cord-263987-ff6kor0c	193	15	formal	formal	JJ
cord-263987-ff6kor0c	193	16	footing	footing	NN
cord-263987-ff6kor0c	193	17	by	by	IN
cord-263987-ff6kor0c	193	18	introducing	introduce	VBG
cord-263987-ff6kor0c	193	19	an	an	DT
cord-263987-ff6kor0c	193	20	explicit	explicit	JJ
cord-263987-ff6kor0c	193	21	notation	notation	NN
cord-263987-ff6kor0c	193	22	for	for	IN
cord-263987-ff6kor0c	193	23	indel	indel	NN
cord-263987-ff6kor0c	193	24	trajectories	trajectory	NNS
cord-263987-ff6kor0c	193	25	and	and	CC
cord-263987-ff6kor0c	193	26	the	the	DT
cord-263987-ff6kor0c	193	27	concept	concept	NN
cord-263987-ff6kor0c	193	28	of	of	IN
cord-263987-ff6kor0c	193	29	"	"	``
cord-263987-ff6kor0c	193	30	local	local	JJ
cord-263987-ff6kor0c	193	31	history	history	NN
cord-263987-ff6kor0c	193	32	set	set	VBD
cord-263987-ff6kor0c	193	33	equivalence	equivalence	NN
cord-263987-ff6kor0c	193	34	classes	class	NNS
cord-263987-ff6kor0c	193	35	"	"	''
cord-263987-ff6kor0c	193	36	for	for	IN
cord-263987-ff6kor0c	193	37	equivalent	equivalent	JJ
cord-263987-ff6kor0c	193	38	trajectories	trajectory	NNS
cord-263987-ff6kor0c	193	39	.	.	.
cord-263987-ff6kor0c	194	1	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	194	2	uses	use	VBZ
cord-263987-ff6kor0c	194	3	this	this	DT
cord-263987-ff6kor0c	194	4	concept	concept	NN
cord-263987-ff6kor0c	194	5	to	to	TO
cord-263987-ff6kor0c	194	6	prove	prove	VB
cord-263987-ff6kor0c	194	7	that	that	DT
cord-263987-ff6kor0c	194	8	alignment	alignment	NN
cord-263987-ff6kor0c	194	9	likelihoods	likelihood	NNS
cord-263987-ff6kor0c	194	10	for	for	IN
cord-263987-ff6kor0c	194	11	long	long	JJ
cord-263987-ff6kor0c	194	12	-	-	HYPH
cord-263987-ff6kor0c	194	13	indel	indel	NN
cord-263987-ff6kor0c	194	14	and	and	CC
cord-263987-ff6kor0c	194	15	related	related	JJ
cord-263987-ff6kor0c	194	16	models	model	NNS
cord-263987-ff6kor0c	194	17	are	be	VBP
cord-263987-ff6kor0c	194	18	indeed	indeed	RB
cord-263987-ff6kor0c	194	19	factorable	factorable	JJ
cord-263987-ff6kor0c	194	20	,	,	,
cord-263987-ff6kor0c	194	21	and	and	CC
cord-263987-ff6kor0c	194	22	investigates	investigate	NNS
cord-263987-ff6kor0c	194	23	,	,	,
cord-263987-ff6kor0c	194	24	by	by	IN
cord-263987-ff6kor0c	194	25	numerical	numerical	JJ
cord-263987-ff6kor0c	194	26	computation	computation	NN
cord-263987-ff6kor0c	194	27	and	and	CC
cord-263987-ff6kor0c	194	28	analysis	analysis	NN
cord-263987-ff6kor0c	194	29	(	(	-LRB-
cord-263987-ff6kor0c	194	30	with	with	IN
cord-263987-ff6kor0c	194	31	confirmation	confirmation	NN
cord-263987-ff6kor0c	194	32	by	by	IN
cord-263987-ff6kor0c	194	33	simulation	simulation	NN
cord-263987-ff6kor0c	194	34	)	)	-RRB-
cord-263987-ff6kor0c	194	35	,	,	,
cord-263987-ff6kor0c	194	36	the	the	DT
cord-263987-ff6kor0c	194	37	relative	relative	JJ
cord-263987-ff6kor0c	194	38	contribution	contribution	NN
cord-263987-ff6kor0c	194	39	of	of	IN
cord-263987-ff6kor0c	194	40	multiple	multiple	JJ
cord-263987-ff6kor0c	194	41	-	-	HYPH
cord-263987-ff6kor0c	194	42	event	event	NN
cord-263987-ff6kor0c	194	43	trajectories	trajectory	NNS
cord-263987-ff6kor0c	194	44	to	to	IN
cord-263987-ff6kor0c	194	45	gap	gap	VB
cord-263987-ff6kor0c	194	46	length	length	NN
cord-263987-ff6kor0c	194	47	distributions	distribution	NNS
cord-263987-ff6kor0c	194	48	.	.	.
cord-263987-ff6kor0c	195	1	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	195	2	's	's	POS
cord-263987-ff6kor0c	195	3	results	result	NNS
cord-263987-ff6kor0c	195	4	also	also	RB
cord-263987-ff6kor0c	195	5	show	show	VBP
cord-263987-ff6kor0c	195	6	that	that	IN
cord-263987-ff6kor0c	195	7	the	the	DT
cord-263987-ff6kor0c	195	8	effects	effect	NNS
cord-263987-ff6kor0c	195	9	on	on	IN
cord-263987-ff6kor0c	195	10	the	the	DT
cord-263987-ff6kor0c	195	11	observed	observed	JJ
cord-263987-ff6kor0c	195	12	indel	indel	NN
cord-263987-ff6kor0c	195	13	lengths	length	NNS
cord-263987-ff6kor0c	195	14	due	due	JJ
cord-263987-ff6kor0c	195	15	to	to	IN
cord-263987-ff6kor0c	195	16	overlapping	overlap	VBG
cord-263987-ff6kor0c	195	17	indels	indel	NNS
cord-263987-ff6kor0c	195	18	become	become	VBP
cord-263987-ff6kor0c	195	19	more	more	RBR
cord-263987-ff6kor0c	195	20	significant	significant	JJ
cord-263987-ff6kor0c	195	21	as	as	IN
cord-263987-ff6kor0c	195	22	the	the	DT
cord-263987-ff6kor0c	195	23	indels	indel	NNS
cord-263987-ff6kor0c	195	24	get	get	VBP
cord-263987-ff6kor0c	195	25	larger	large	JJR
cord-263987-ff6kor0c	195	26	,	,	,
cord-263987-ff6kor0c	195	27	making	make	VBG
cord-263987-ff6kor0c	195	28	the	the	DT
cord-263987-ff6kor0c	195	29	problem	problem	NN
cord-263987-ff6kor0c	195	30	particularly	particularly	RB
cord-263987-ff6kor0c	195	31	acute	acute	JJ
cord-263987-ff6kor0c	195	32	for	for	IN
cord-263987-ff6kor0c	195	33	genomic	genomic	JJ
cord-263987-ff6kor0c	195	34	alignments	alignment	NNS
cord-263987-ff6kor0c	195	35	where	where	WRB
cord-263987-ff6kor0c	195	36	indels	indel	NNS
cord-263987-ff6kor0c	195	37	can	can	MD
cord-263987-ff6kor0c	195	38	be	be	VB
cord-263987-ff6kor0c	195	39	much	much	RB
cord-263987-ff6kor0c	195	40	larger	large	JJR
cord-263987-ff6kor0c	195	41	than	than	IN
cord-263987-ff6kor0c	195	42	in	in	IN
cord-263987-ff6kor0c	195	43	proteins	protein	NNS
cord-263987-ff6kor0c	195	44	.	.	.
cord-263987-ff6kor0c	196	1	A	a	DT
cord-263987-ff6kor0c	196	2	number	number	NN
cord-263987-ff6kor0c	196	3	of	of	IN
cord-263987-ff6kor0c	196	4	excellent	excellent	JJ
cord-263987-ff6kor0c	196	5	,	,	,
cord-263987-ff6kor0c	196	6	realistic	realistic	JJ
cord-263987-ff6kor0c	196	7	sequence	sequence	NN
cord-263987-ff6kor0c	196	8	simulators	simulator	NNS
cord-263987-ff6kor0c	196	9	are	be	VBP
cord-263987-ff6kor0c	196	10	available	available	JJ
cord-263987-ff6kor0c	196	11	including	include	VBG
cord-263987-ff6kor0c	196	12	DAWG	DAWG	NNP
cord-263987-ff6kor0c	196	13	[	[	-LRB-
cord-263987-ff6kor0c	196	14	99	99	CD
cord-263987-ff6kor0c	196	15	]	]	-RRB-
cord-263987-ff6kor0c	196	16	,	,	,
cord-263987-ff6kor0c	196	17	INDELible	indelible	JJ
cord-263987-ff6kor0c	196	18	[	[	-LRB-
cord-263987-ff6kor0c	196	19	100	100	CD
cord-263987-ff6kor0c	196	20	]	]	-RRB-
cord-263987-ff6kor0c	196	21	,	,	,
cord-263987-ff6kor0c	196	22	and	and	CC
cord-263987-ff6kor0c	196	23	indel	indel	NN
cord-263987-ff6kor0c	196	24	-	-	HYPH
cord-263987-ff6kor0c	196	25	Seq	seq	NN
cord-263987-ff6kor0c	196	26	-	-	HYPH
cord-263987-ff6kor0c	196	27	Gen	Gen	NNP
cord-263987-ff6kor0c	196	28	[	[	-LRB-
cord-263987-ff6kor0c	196	29	101	101	CD
cord-263987-ff6kor0c	196	30	]	]	-RRB-
cord-263987-ff6kor0c	196	31	.	.	.
cord-263987-ff6kor0c	197	1	Consider	consider	VB
cord-263987-ff6kor0c	197	2	now	now	RB
cord-263987-ff6kor0c	197	3	the	the	DT
cord-263987-ff6kor0c	197	4	extension	extension	NN
cord-263987-ff6kor0c	197	5	of	of	IN
cord-263987-ff6kor0c	197	6	these	these	DT
cord-263987-ff6kor0c	197	7	results	result	NNS
cord-263987-ff6kor0c	197	8	from	from	IN
cord-263987-ff6kor0c	197	9	pairwise	pairwise	JJ
cord-263987-ff6kor0c	197	10	alignments	alignment	NNS
cord-263987-ff6kor0c	197	11	,	,	,
cord-263987-ff6kor0c	197	12	such	such	JJ
cord-263987-ff6kor0c	197	13	as	as	IN
cord-263987-ff6kor0c	197	14	TKF91	TKF91	NNP
cord-263987-ff6kor0c	197	15	and	and	CC
cord-263987-ff6kor0c	197	16	the	the	DT
cord-263987-ff6kor0c	197	17	"	"	``
cord-263987-ff6kor0c	197	18	long	long	JJ
cord-263987-ff6kor0c	197	19	indel	indel	NN
cord-263987-ff6kor0c	197	20	"	"	''
cord-263987-ff6kor0c	197	21	model	model	NN
cord-263987-ff6kor0c	197	22	,	,	,
cord-263987-ff6kor0c	197	23	to	to	IN
cord-263987-ff6kor0c	197	24	multiple	multiple	JJ
cord-263987-ff6kor0c	197	25	alignments	alignment	NNS
cord-263987-ff6kor0c	197	26	(	(	-LRB-
cord-263987-ff6kor0c	197	27	with	with	IN
cord-263987-ff6kor0c	197	28	associated	associated	JJ
cord-263987-ff6kor0c	197	29	phylogenies	phylogeny	NNS
cord-263987-ff6kor0c	197	30	)	)	-RRB-
cord-263987-ff6kor0c	197	31	.	.	.
cord-263987-ff6kor0c	198	1	Some	some	DT
cord-263987-ff6kor0c	198	2	of	of	IN
cord-263987-ff6kor0c	198	3	the	the	DT
cord-263987-ff6kor0c	198	4	approaches	approach	NNS
cord-263987-ff6kor0c	198	5	to	to	IN
cord-263987-ff6kor0c	198	6	this	this	DT
cord-263987-ff6kor0c	198	7	problem	problem	NN
cord-263987-ff6kor0c	198	8	use	use	VBP
cord-263987-ff6kor0c	198	9	Markov	Markov	NNP
cord-263987-ff6kor0c	198	10	Chain	Chain	NNP
cord-263987-ff6kor0c	198	11	Monte	Monte	NNP
cord-263987-ff6kor0c	198	12	Carlo	Carlo	NNP
cord-263987-ff6kor0c	198	13	(	(	-LRB-
cord-263987-ff6kor0c	198	14	MCMC	MCMC	NNP
cord-263987-ff6kor0c	198	15	)	)	-RRB-
cord-263987-ff6kor0c	198	16	;	;	:
cord-263987-ff6kor0c	198	17	some	some	DT
cord-263987-ff6kor0c	198	18	of	of	IN
cord-263987-ff6kor0c	198	19	the	the	DT
cord-263987-ff6kor0c	198	20	approaches	approach	NNS
cord-263987-ff6kor0c	198	21	use	use	VBP
cord-263987-ff6kor0c	198	22	finite	finite	JJ
cord-263987-ff6kor0c	198	23	-	-	HYPH
cord-263987-ff6kor0c	198	24	state	state	NN
cord-263987-ff6kor0c	198	25	automata	automaton	NNS
cord-263987-ff6kor0c	198	26	;	;	:
cord-263987-ff6kor0c	198	27	and	and	CC
cord-263987-ff6kor0c	198	28	there	there	EX
cord-263987-ff6kor0c	198	29	is	be	VBZ
cord-263987-ff6kor0c	198	30	also	also	RB
cord-263987-ff6kor0c	198	31	some	some	DT
cord-263987-ff6kor0c	198	32	overlap	overlap	VBP
cord-263987-ff6kor0c	198	33	between	between	IN
cord-263987-ff6kor0c	198	34	these	these	DT
cord-263987-ff6kor0c	198	35	categories	category	NNS
cord-263987-ff6kor0c	199	1	(	(	-LRB-
cord-263987-ff6kor0c	199	2	i.e.	i.e.	FW
cord-263987-ff6kor0c	199	3	MCMC	MCMC	NNP
cord-263987-ff6kor0c	199	4	approaches	approach	VBZ
cord-263987-ff6kor0c	199	5	that	that	WDT
cord-263987-ff6kor0c	199	6	use	use	VBP
cord-263987-ff6kor0c	199	7	automata	automata	NN
cord-263987-ff6kor0c	199	8	)	)	-RRB-
cord-263987-ff6kor0c	199	9	.	.	.
cord-263987-ff6kor0c	200	1	MCMC	MCMC	NNP
cord-263987-ff6kor0c	200	2	is	be	VBZ
cord-263987-ff6kor0c	200	3	the	the	DT
cord-263987-ff6kor0c	200	4	most	most	RBS
cord-263987-ff6kor0c	200	5	principled	principled	JJ
cord-263987-ff6kor0c	200	6	approach	approach	NN
cord-263987-ff6kor0c	200	7	to	to	IN
cord-263987-ff6kor0c	200	8	integrating	integrate	VBG
cord-263987-ff6kor0c	200	9	phylogeny	phylogeny	NN
cord-263987-ff6kor0c	200	10	with	with	IN
cord-263987-ff6kor0c	200	11	multiple	multiple	JJ
cord-263987-ff6kor0c	200	12	alignment	alignment	NN
cord-263987-ff6kor0c	200	13	.	.	.
cord-263987-ff6kor0c	201	1	In	in	IN
cord-263987-ff6kor0c	201	2	principle	principle	NN
cord-263987-ff6kor0c	201	3	an	an	DT
cord-263987-ff6kor0c	201	4	MCMC	MCMC	NNP
cord-263987-ff6kor0c	201	5	algorithm	algorithm	NN
cord-263987-ff6kor0c	201	6	for	for	IN
cord-263987-ff6kor0c	201	7	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	201	8	alignment	alignment	NN
cord-263987-ff6kor0c	201	9	can	can	MD
cord-263987-ff6kor0c	201	10	yield	yield	VB
cord-263987-ff6kor0c	201	11	the	the	DT
cord-263987-ff6kor0c	201	12	posterior	posterior	JJ
cord-263987-ff6kor0c	201	13	distribution	distribution	NN
cord-263987-ff6kor0c	201	14	of	of	IN
cord-263987-ff6kor0c	201	15	alignments	alignment	NNS
cord-263987-ff6kor0c	201	16	,	,	,
cord-263987-ff6kor0c	201	17	trees	tree	NNS
cord-263987-ff6kor0c	201	18	,	,	,
cord-263987-ff6kor0c	201	19	and	and	CC
cord-263987-ff6kor0c	201	20	parameters	parameter	NNS
cord-263987-ff6kor0c	201	21	for	for	IN
cord-263987-ff6kor0c	201	22	any	any	DT
cord-263987-ff6kor0c	201	23	model	model	NN
cord-263987-ff6kor0c	201	24	whose	whose	WP$
cord-263987-ff6kor0c	201	25	pairwise	pairwise	JJ
cord-263987-ff6kor0c	201	26	distribution	distribution	NN
cord-263987-ff6kor0c	201	27	can	can	MD
cord-263987-ff6kor0c	201	28	be	be	VB
cord-263987-ff6kor0c	201	29	computed	compute	VBN
cord-263987-ff6kor0c	201	30	.	.	.
cord-263987-ff6kor0c	202	1	This	this	DT
cord-263987-ff6kor0c	202	2	includes	include	VBZ
cord-263987-ff6kor0c	202	3	long	long	JJ
cord-263987-ff6kor0c	202	4	indel	indel	NN
cord-263987-ff6kor0c	202	5	models	model	NNS
cord-263987-ff6kor0c	202	6	and	and	CC
cord-263987-ff6kor0c	202	7	also	also	RB
cord-263987-ff6kor0c	202	8	,	,	,
cord-263987-ff6kor0c	202	9	in	in	IN
cord-263987-ff6kor0c	202	10	principle	principle	NN
cord-263987-ff6kor0c	202	11	,	,	,
cord-263987-ff6kor0c	202	12	other	other	JJ
cord-263987-ff6kor0c	202	13	effects	effect	NNS
cord-263987-ff6kor0c	202	14	such	such	JJ
cord-263987-ff6kor0c	202	15	as	as	IN
cord-263987-ff6kor0c	202	16	context	context	NN
cord-263987-ff6kor0c	202	17	-	-	HYPH
cord-263987-ff6kor0c	202	18	dependent	dependent	JJ
cord-263987-ff6kor0c	202	19	substitutions	substitution	NNS
cord-263987-ff6kor0c	202	20	.	.	.
cord-263987-ff6kor0c	203	1	Of	of	IN
cord-263987-ff6kor0c	203	2	the	the	DT
cord-263987-ff6kor0c	203	3	MCMC	MCMC	NNP
cord-263987-ff6kor0c	203	4	methods	method	NNS
cord-263987-ff6kor0c	203	5	reported	report	VBN
cord-263987-ff6kor0c	203	6	in	in	IN
cord-263987-ff6kor0c	203	7	the	the	DT
cord-263987-ff6kor0c	203	8	literature	literature	NN
cord-263987-ff6kor0c	203	9	,	,	,
cord-263987-ff6kor0c	203	10	some	some	DT
cord-263987-ff6kor0c	203	11	just	just	RB
cord-263987-ff6kor0c	203	12	focus	focus	VBP
cord-263987-ff6kor0c	203	13	on	on	IN
cord-263987-ff6kor0c	203	14	alignment	alignment	NN
cord-263987-ff6kor0c	203	15	and	and	CC
cord-263987-ff6kor0c	203	16	ancestral	ancestral	JJ
cord-263987-ff6kor0c	203	17	sequence	sequence	NN
cord-263987-ff6kor0c	203	18	reconstruction	reconstruction	NN
cord-263987-ff6kor0c	203	19	[	[	-LRB-
cord-263987-ff6kor0c	203	20	65	65	CD
cord-263987-ff6kor0c	203	21	]	]	-RRB-
cord-263987-ff6kor0c	203	22	;	;	:
cord-263987-ff6kor0c	203	23	others	other	NNS
cord-263987-ff6kor0c	203	24	on	on	IN
cord-263987-ff6kor0c	203	25	simultaneous	simultaneous	JJ
cord-263987-ff6kor0c	203	26	alignment	alignment	NN
cord-263987-ff6kor0c	203	27	and	and	CC
cord-263987-ff6kor0c	203	28	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	203	29	reconstruction	reconstruction	NN
cord-263987-ff6kor0c	203	30	[	[	-LRB-
cord-263987-ff6kor0c	203	31	79	79	CD
cord-263987-ff6kor0c	203	32	-	-	SYM
cord-263987-ff6kor0c	203	33	81	81	CD
cord-263987-ff6kor0c	203	34	,	,	,
cord-263987-ff6kor0c	203	35	83	83	CD
cord-263987-ff6kor0c	203	36	,	,	,
cord-263987-ff6kor0c	203	37	102	102	CD
cord-263987-ff6kor0c	203	38	,	,	,
cord-263987-ff6kor0c	203	39	103	103	CD
cord-263987-ff6kor0c	203	40	]	]	-RRB-
cord-263987-ff6kor0c	203	41	;	;	:
cord-263987-ff6kor0c	203	42	some	some	DT
cord-263987-ff6kor0c	203	43	also	also	RB
cord-263987-ff6kor0c	203	44	include	include	VBP
cord-263987-ff6kor0c	203	45	estimation	estimation	NN
cord-263987-ff6kor0c	203	46	of	of	IN
cord-263987-ff6kor0c	203	47	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	203	48	parameters	parameter	NNS
cord-263987-ff6kor0c	203	49	such	such	JJ
cord-263987-ff6kor0c	203	50	as	as	IN
cord-263987-ff6kor0c	203	51	dN	dN	NNP
cord-263987-ff6kor0c	203	52	/	/	SYM
cord-263987-ff6kor0c	203	53	dS	ds	NN
cord-263987-ff6kor0c	203	54	[	[	-LRB-
cord-263987-ff6kor0c	203	55	104	104	CD
cord-263987-ff6kor0c	203	56	]	]	-RRB-
cord-263987-ff6kor0c	203	57	;	;	:
cord-263987-ff6kor0c	203	58	and	and	CC
cord-263987-ff6kor0c	203	59	some	some	DT
cord-263987-ff6kor0c	203	60	(	(	-LRB-
cord-263987-ff6kor0c	203	61	focused	focus	VBN
cord-263987-ff6kor0c	203	62	on	on	IN
cord-263987-ff6kor0c	203	63	RNA	RNA	NNP
cord-263987-ff6kor0c	203	64	sequences	sequence	NNS
cord-263987-ff6kor0c	203	65	)	)	-RRB-
cord-263987-ff6kor0c	203	66	attempt	attempt	VBP
cord-263987-ff6kor0c	203	67	prediction	prediction	NN
cord-263987-ff6kor0c	203	68	of	of	IN
cord-263987-ff6kor0c	203	69	secondary	secondary	JJ
cord-263987-ff6kor0c	203	70	structure	structure	NN
cord-263987-ff6kor0c	203	71	[	[	-LRB-
cord-263987-ff6kor0c	203	72	105	105	CD
cord-263987-ff6kor0c	203	73	,	,	,
cord-263987-ff6kor0c	203	74	106	106	CD
cord-263987-ff6kor0c	203	75	]	]	-RRB-
cord-263987-ff6kor0c	203	76	.	.	.
cord-263987-ff6kor0c	204	1	In	in	IN
cord-263987-ff6kor0c	204	2	practise	practise	NN
cord-263987-ff6kor0c	204	3	these	these	DT
cord-263987-ff6kor0c	204	4	mostly	mostly	RB
cord-263987-ff6kor0c	204	5	use	use	VBP
cord-263987-ff6kor0c	204	6	HMMs	HMMs	NNP
cord-263987-ff6kor0c	204	7	,	,	,
cord-263987-ff6kor0c	204	8	or	or	CC
cord-263987-ff6kor0c	204	9	dynamic	dynamic	JJ
cord-263987-ff6kor0c	204	10	programming	programming	NN
cord-263987-ff6kor0c	204	11	of	of	IN
cord-263987-ff6kor0c	204	12	some	some	DT
cord-263987-ff6kor0c	204	13	form	form	NN
cord-263987-ff6kor0c	204	14	,	,	,
cord-263987-ff6kor0c	204	15	in	in	IN
cord-263987-ff6kor0c	204	16	common	common	JJ
cord-263987-ff6kor0c	204	17	with	with	IN
cord-263987-ff6kor0c	204	18	the	the	DT
cord-263987-ff6kor0c	204	19	methods	method	NNS
cord-263987-ff6kor0c	204	20	of	of	IN
cord-263987-ff6kor0c	204	21	the	the	DT
cord-263987-ff6kor0c	204	22	following	following	JJ
cord-263987-ff6kor0c	204	23	section	section	NN
cord-263987-ff6kor0c	204	24	.	.	.
cord-263987-ff6kor0c	205	1	It	-PRON-	PRP
cord-263987-ff6kor0c	205	2	is	be	VBZ
cord-263987-ff6kor0c	205	3	of	of	IN
cord-263987-ff6kor0c	205	4	course	course	NN
cord-263987-ff6kor0c	205	5	possible	possible	JJ
cord-263987-ff6kor0c	205	6	to	to	TO
cord-263987-ff6kor0c	205	7	use	use	VB
cord-263987-ff6kor0c	205	8	HMM	HMM	NNP
cord-263987-ff6kor0c	205	9	-	-	HYPH
cord-263987-ff6kor0c	205	10	based	base	VBN
cord-263987-ff6kor0c	205	11	or	or	CC
cord-263987-ff6kor0c	205	12	other	other	JJ
cord-263987-ff6kor0c	205	13	MCMC	MCMC	NNP
cord-263987-ff6kor0c	205	14	approaches	approach	NNS
cord-263987-ff6kor0c	205	15	to	to	TO
cord-263987-ff6kor0c	205	16	propose	propose	VB
cord-263987-ff6kor0c	205	17	candidate	candidate	NN
cord-263987-ff6kor0c	205	18	reconstructions	reconstruction	NNS
cord-263987-ff6kor0c	205	19	,	,	,
cord-263987-ff6kor0c	205	20	and	and	CC
cord-263987-ff6kor0c	205	21	then	then	RB
cord-263987-ff6kor0c	205	22	to	to	TO
cord-263987-ff6kor0c	205	23	accept	accept	VB
cord-263987-ff6kor0c	205	24	or	or	CC
cord-263987-ff6kor0c	205	25	reject	reject	VB
cord-263987-ff6kor0c	205	26	those	those	DT
cord-263987-ff6kor0c	205	27	proposals	proposal	NNS
cord-263987-ff6kor0c	205	28	(	(	-LRB-
cord-263987-ff6kor0c	205	29	in	in	IN
cord-263987-ff6kor0c	205	30	the	the	DT
cord-263987-ff6kor0c	205	31	manner	manner	NN
cord-263987-ff6kor0c	205	32	of	of	IN
cord-263987-ff6kor0c	205	33	Metropolis	Metropolis	NNP
cord-263987-ff6kor0c	205	34	-	-	HYPH
cord-263987-ff6kor0c	205	35	Hastings	Hastings	NNP
cord-263987-ff6kor0c	205	36	or	or	CC
cord-263987-ff6kor0c	205	37	importance	importance	NN
cord-263987-ff6kor0c	205	38	sampling	sampling	NN
cord-263987-ff6kor0c	205	39	)	)	-RRB-
cord-263987-ff6kor0c	205	40	using	use	VBG
cord-263987-ff6kor0c	205	41	a	a	DT
cord-263987-ff6kor0c	205	42	more	more	RBR
cord-263987-ff6kor0c	205	43	realistic	realistic	JJ
cord-263987-ff6kor0c	205	44	formulation	formulation	NN
cord-263987-ff6kor0c	205	45	of	of	IN
cord-263987-ff6kor0c	205	46	the	the	DT
cord-263987-ff6kor0c	205	47	indel	indel	NN
cord-263987-ff6kor0c	205	48	likelihood	likelihood	NN
cord-263987-ff6kor0c	205	49	.	.	.
cord-263987-ff6kor0c	206	1	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	206	2	's	's	POS
cord-263987-ff6kor0c	206	3	methods	method	NNS
cord-263987-ff6kor0c	206	4	,	,	,
cord-263987-ff6kor0c	206	5	and	and	CC
cord-263987-ff6kor0c	206	6	others	other	NNS
cord-263987-ff6kor0c	206	7	that	that	WDT
cord-263987-ff6kor0c	206	8	build	build	VBP
cord-263987-ff6kor0c	206	9	on	on	IN
cord-263987-ff6kor0c	206	10	them	-PRON-	PRP
cord-263987-ff6kor0c	206	11	or	or	CC
cord-263987-ff6kor0c	206	12	are	be	VBP
cord-263987-ff6kor0c	206	13	related	relate	VBN
cord-263987-ff6kor0c	206	14	to	to	IN
cord-263987-ff6kor0c	206	15	them	-PRON-	PRP
cord-263987-ff6kor0c	206	16	,	,	,
cord-263987-ff6kor0c	206	17	may	may	MD
cord-263987-ff6kor0c	206	18	be	be	VB
cord-263987-ff6kor0c	206	19	useful	useful	JJ
cord-263987-ff6kor0c	206	20	in	in	IN
cord-263987-ff6kor0c	206	21	this	this	DT
cord-263987-ff6kor0c	206	22	context	context	NN
cord-263987-ff6kor0c	206	23	.	.	.
cord-263987-ff6kor0c	207	1	For	for	IN
cord-263987-ff6kor0c	207	2	example	example	NN
cord-263987-ff6kor0c	207	3	,	,	,
cord-263987-ff6kor0c	207	4	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	207	5	's	's	POS
cord-263987-ff6kor0c	207	6	formulation	formulation	NN
cord-263987-ff6kor0c	207	7	was	be	VBD
cord-263987-ff6kor0c	207	8	used	use	VBN
cord-263987-ff6kor0c	207	9	to	to	TO
cord-263987-ff6kor0c	207	10	calculate	calculate	VB
cord-263987-ff6kor0c	207	11	the	the	DT
cord-263987-ff6kor0c	207	12	indel	indel	NN
cord-263987-ff6kor0c	207	13	component	component	NN
cord-263987-ff6kor0c	207	14	of	of	IN
cord-263987-ff6kor0c	207	15	the	the	DT
cord-263987-ff6kor0c	207	16	probability	probability	NN
cord-263987-ff6kor0c	207	17	of	of	IN
cord-263987-ff6kor0c	207	18	a	a	DT
cord-263987-ff6kor0c	207	19	fixed	fix	VBN
cord-263987-ff6kor0c	207	20	multiple	multiple	JJ
cord-263987-ff6kor0c	207	21	sequence	sequence	NN
cord-263987-ff6kor0c	207	22	alignment	alignment	NN
cord-263987-ff6kor0c	207	23	(	(	-LRB-
cord-263987-ff6kor0c	207	24	MSA	MSA	NNP
cord-263987-ff6kor0c	207	25	)	)	-RRB-
cord-263987-ff6kor0c	207	26	resulting	result	VBG
cord-263987-ff6kor0c	207	27	from	from	IN
cord-263987-ff6kor0c	207	28	sequence	sequence	NN
cord-263987-ff6kor0c	207	29	evolution	evolution	NN
cord-263987-ff6kor0c	207	30	along	along	IN
cord-263987-ff6kor0c	207	31	a	a	DT
cord-263987-ff6kor0c	207	32	fixed	fix	VBN
cord-263987-ff6kor0c	207	33	tree	tree	NN
cord-263987-ff6kor0c	207	34	[	[	-LRB-
cord-263987-ff6kor0c	207	35	53	53	CD
cord-263987-ff6kor0c	207	36	]	]	-RRB-
cord-263987-ff6kor0c	207	37	.	.	.
cord-263987-ff6kor0c	208	1	He	-PRON-	PRP
cord-263987-ff6kor0c	208	2	also	also	RB
cord-263987-ff6kor0c	208	3	developed	develop	VBD
cord-263987-ff6kor0c	208	4	an	an	DT
cord-263987-ff6kor0c	208	5	algorithm	algorithm	NN
cord-263987-ff6kor0c	208	6	to	to	TO
cord-263987-ff6kor0c	208	7	approximately	approximately	RB
cord-263987-ff6kor0c	208	8	calculate	calculate	VB
cord-263987-ff6kor0c	208	9	the	the	DT
cord-263987-ff6kor0c	208	10	indel	indel	NN
cord-263987-ff6kor0c	208	11	component	component	NN
cord-263987-ff6kor0c	208	12	of	of	IN
cord-263987-ff6kor0c	208	13	the	the	DT
cord-263987-ff6kor0c	208	14	MSA	MSA	NNP
cord-263987-ff6kor0c	208	15	probability	probability	NN
cord-263987-ff6kor0c	208	16	using	use	VBG
cord-263987-ff6kor0c	208	17	all	all	DT
cord-263987-ff6kor0c	208	18	MSAcompatible	msacompatible	JJ
cord-263987-ff6kor0c	208	19	parsimonious	parsimonious	JJ
cord-263987-ff6kor0c	208	20	indel	indel	NN
cord-263987-ff6kor0c	208	21	histories	history	NNS
cord-263987-ff6kor0c	208	22	[	[	-LRB-
cord-263987-ff6kor0c	208	23	54	54	CD
cord-263987-ff6kor0c	208	24	]	]	-RRB-
cord-263987-ff6kor0c	208	25	,	,	,
cord-263987-ff6kor0c	208	26	and	and	CC
cord-263987-ff6kor0c	208	27	applied	apply	VBD
cord-263987-ff6kor0c	208	28	it	-PRON-	PRP
cord-263987-ff6kor0c	208	29	to	to	IN
cord-263987-ff6kor0c	208	30	some	some	DT
cord-263987-ff6kor0c	208	31	analyses	analysis	NNS
cord-263987-ff6kor0c	208	32	of	of	IN
cord-263987-ff6kor0c	208	33	simulated	simulated	JJ
cord-263987-ff6kor0c	208	34	MSAs	msa	NNS
cord-263987-ff6kor0c	208	35	[	[	-LRB-
cord-263987-ff6kor0c	208	36	107	107	CD
cord-263987-ff6kor0c	208	37	]	]	-RRB-
cord-263987-ff6kor0c	208	38	.	.	.
cord-263987-ff6kor0c	209	1	Using	use	VBG
cord-263987-ff6kor0c	209	2	such	such	JJ
cord-263987-ff6kor0c	209	3	realistic	realistic	JJ
cord-263987-ff6kor0c	209	4	likelihood	likelihood	NN
cord-263987-ff6kor0c	209	5	calculations	calculation	NNS
cord-263987-ff6kor0c	209	6	as	as	IN
cord-263987-ff6kor0c	209	7	a	a	DT
cord-263987-ff6kor0c	209	8	post	post	JJ
cord-263987-ff6kor0c	209	9	-	-	JJ
cord-263987-ff6kor0c	209	10	processing	processing	JJ
cord-263987-ff6kor0c	209	11	"	"	``
cord-263987-ff6kor0c	209	12	filter	filter	NN
cord-263987-ff6kor0c	209	13	"	"	''
cord-263987-ff6kor0c	209	14	for	for	IN
cord-263987-ff6kor0c	209	15	coarser	coarser	NN
cord-263987-ff6kor0c	209	16	,	,	,
cord-263987-ff6kor0c	209	17	more	more	RBR
cord-263987-ff6kor0c	209	18	rapid	rapid	JJ
cord-263987-ff6kor0c	209	19	MCMC	MCMC	NNP
cord-263987-ff6kor0c	209	20	approaches	approach	VBZ
cord-263987-ff6kor0c	209	21	that	that	WDT
cord-263987-ff6kor0c	209	22	sample	sample	VBP
cord-263987-ff6kor0c	209	23	the	the	DT
cord-263987-ff6kor0c	209	24	space	space	NN
cord-263987-ff6kor0c	209	25	of	of	IN
cord-263987-ff6kor0c	209	26	possible	possible	JJ
cord-263987-ff6kor0c	209	27	reconstructions	reconstruction	NNS
cord-263987-ff6kor0c	209	28	could	could	MD
cord-263987-ff6kor0c	209	29	be	be	VB
cord-263987-ff6kor0c	209	30	a	a	DT
cord-263987-ff6kor0c	209	31	promising	promising	JJ
cord-263987-ff6kor0c	209	32	approach	approach	NN
cord-263987-ff6kor0c	209	33	.	.	.
cord-263987-ff6kor0c	210	1	The	the	DT
cord-263987-ff6kor0c	210	2	dynamic	dynamic	JJ
cord-263987-ff6kor0c	210	3	programming	programming	NN
cord-263987-ff6kor0c	210	4	recursion	recursion	NN
cord-263987-ff6kor0c	210	5	for	for	IN
cord-263987-ff6kor0c	210	6	pairwise	pairwise	JJ
cord-263987-ff6kor0c	210	7	alignment	alignment	NN
cord-263987-ff6kor0c	210	8	reported	report	VBN
cord-263987-ff6kor0c	210	9	for	for	IN
cord-263987-ff6kor0c	210	10	the	the	DT
cord-263987-ff6kor0c	210	11	TKF91	TKF91	NNP
cord-263987-ff6kor0c	210	12	model	model	NN
cord-263987-ff6kor0c	210	13	[	[	-LRB-
cord-263987-ff6kor0c	210	14	63	63	CD
cord-263987-ff6kor0c	210	15	]	]	-RRB-
cord-263987-ff6kor0c	210	16	can	can	MD
cord-263987-ff6kor0c	210	17	be	be	VB
cord-263987-ff6kor0c	210	18	exactly	exactly	RB
cord-263987-ff6kor0c	210	19	extended	extend	VBN
cord-263987-ff6kor0c	210	20	to	to	IN
cord-263987-ff6kor0c	210	21	alignment	alignment	NN
cord-263987-ff6kor0c	210	22	of	of	IN
cord-263987-ff6kor0c	210	23	multiple	multiple	JJ
cord-263987-ff6kor0c	210	24	sequences	sequence	NNS
cord-263987-ff6kor0c	210	25	given	give	VBN
cord-263987-ff6kor0c	210	26	a	a	DT
cord-263987-ff6kor0c	210	27	tree	tree	NN
cord-263987-ff6kor0c	210	28	[	[	-LRB-
cord-263987-ff6kor0c	210	29	108	108	CD
cord-263987-ff6kor0c	210	30	,	,	,
cord-263987-ff6kor0c	210	31	109	109	CD
cord-263987-ff6kor0c	210	32	]	]	-RRB-
cord-263987-ff6kor0c	210	33	.	.	.
cord-263987-ff6kor0c	211	1	This	this	DT
cord-263987-ff6kor0c	211	2	works	work	VBZ
cord-263987-ff6kor0c	211	3	essentially	essentially	RB
cord-263987-ff6kor0c	211	4	because	because	IN
cord-263987-ff6kor0c	211	5	the	the	DT
cord-263987-ff6kor0c	211	6	TKF91	TKF91	NNP
cord-263987-ff6kor0c	211	7	joint	joint	JJ
cord-263987-ff6kor0c	211	8	distribution	distribution	NN
cord-263987-ff6kor0c	211	9	over	over	IN
cord-263987-ff6kor0c	211	10	ancestor	ancestor	NN
cord-263987-ff6kor0c	211	11	and	and	CC
cord-263987-ff6kor0c	211	12	descendant	descendant	JJ
cord-263987-ff6kor0c	211	13	sequences	sequence	NNS
cord-263987-ff6kor0c	211	14	can	can	MD
cord-263987-ff6kor0c	211	15	be	be	VB
cord-263987-ff6kor0c	211	16	represented	represent	VBN
cord-263987-ff6kor0c	211	17	as	as	IN
cord-263987-ff6kor0c	211	18	a	a	DT
cord-263987-ff6kor0c	211	19	Pair	pair	NN
cord-263987-ff6kor0c	211	20	HMM	HMM	NNP
cord-263987-ff6kor0c	211	21	;	;	:
cord-263987-ff6kor0c	211	22	the	the	DT
cord-263987-ff6kor0c	211	23	multiple	multiple	JJ
cord-263987-ff6kor0c	211	24	-	-	HYPH
cord-263987-ff6kor0c	211	25	sequence	sequence	NN
cord-263987-ff6kor0c	211	26	version	version	NN
cord-263987-ff6kor0c	211	27	is	be	VBZ
cord-263987-ff6kor0c	211	28	a	a	DT
cord-263987-ff6kor0c	211	29	multi	multi	JJ
cord-263987-ff6kor0c	211	30	-	-	JJ
cord-263987-ff6kor0c	211	31	sequence	sequence	NN
cord-263987-ff6kor0c	212	1	HMM	hmm	UH
cord-263987-ff6kor0c	212	2	[	[	-LRB-
cord-263987-ff6kor0c	212	3	65	65	CD
cord-263987-ff6kor0c	212	4	]	]	-RRB-
cord-263987-ff6kor0c	212	5	.	.	.
cord-263987-ff6kor0c	213	1	This	this	DT
cord-263987-ff6kor0c	213	2	approach	approach	NN
cord-263987-ff6kor0c	213	3	can	can	MD
cord-263987-ff6kor0c	213	4	be	be	VB
cord-263987-ff6kor0c	213	5	generalized	generalize	VBN
cord-263987-ff6kor0c	213	6	,	,	,
cord-263987-ff6kor0c	213	7	using	use	VBG
cord-263987-ff6kor0c	213	8	finite	finite	JJ
cord-263987-ff6kor0c	213	9	-	-	HYPH
cord-263987-ff6kor0c	213	10	state	state	NN
cord-263987-ff6kor0c	213	11	transducer	transducer	NN
cord-263987-ff6kor0c	213	12	theory	theory	NN
cord-263987-ff6kor0c	213	13	.	.	.
cord-263987-ff6kor0c	214	1	Transducers	transducer	NNS
cord-263987-ff6kor0c	214	2	were	be	VBD
cord-263987-ff6kor0c	214	3	originally	originally	RB
cord-263987-ff6kor0c	214	4	developed	develop	VBN
cord-263987-ff6kor0c	214	5	as	as	IN
cord-263987-ff6kor0c	214	6	modular	modular	JJ
cord-263987-ff6kor0c	214	7	representations	representation	NNS
cord-263987-ff6kor0c	214	8	of	of	IN
cord-263987-ff6kor0c	214	9	sequence	sequence	NN
cord-263987-ff6kor0c	214	10	-	-	HYPH
cord-263987-ff6kor0c	214	11	transforming	transform	VBG
cord-263987-ff6kor0c	214	12	operations	operation	NNS
cord-263987-ff6kor0c	214	13	for	for	IN
cord-263987-ff6kor0c	214	14	use	use	NN
cord-263987-ff6kor0c	214	15	in	in	IN
cord-263987-ff6kor0c	214	16	speech	speech	NN
cord-263987-ff6kor0c	214	17	recognition	recognition	NN
cord-263987-ff6kor0c	214	18	[	[	-LRB-
cord-263987-ff6kor0c	214	19	110	110	CD
cord-263987-ff6kor0c	214	20	]	]	-RRB-
cord-263987-ff6kor0c	214	21	.	.	.
cord-263987-ff6kor0c	215	1	In	in	IN
cord-263987-ff6kor0c	215	2	bioinformatics	bioinformatic	NNS
cord-263987-ff6kor0c	215	3	,	,	,
cord-263987-ff6kor0c	215	4	they	-PRON-	PRP
cord-263987-ff6kor0c	215	5	offer	offer	VBP
cord-263987-ff6kor0c	215	6	(	(	-LRB-
cord-263987-ff6kor0c	215	7	among	among	IN
cord-263987-ff6kor0c	215	8	other	other	JJ
cord-263987-ff6kor0c	215	9	things	thing	NNS
cord-263987-ff6kor0c	215	10	)	)	-RRB-
cord-263987-ff6kor0c	215	11	a	a	DT
cord-263987-ff6kor0c	215	12	systematic	systematic	JJ
cord-263987-ff6kor0c	215	13	way	way	NN
cord-263987-ff6kor0c	215	14	of	of	IN
cord-263987-ff6kor0c	215	15	extending	extend	VBG
cord-263987-ff6kor0c	215	16	HMM	HMM	NNP
cord-263987-ff6kor0c	215	17	-	-	HYPH
cord-263987-ff6kor0c	215	18	like	like	JJ
cord-263987-ff6kor0c	215	19	pairwise	pairwise	JJ
cord-263987-ff6kor0c	215	20	alignment	alignment	NN
cord-263987-ff6kor0c	215	21	likelihoods	likelihood	NNS
cord-263987-ff6kor0c	215	22	to	to	IN
cord-263987-ff6kor0c	215	23	trees	tree	NNS
cord-263987-ff6kor0c	215	24	[	[	-LRB-
cord-263987-ff6kor0c	215	25	67	67	CD
cord-263987-ff6kor0c	215	26	,	,	,
cord-263987-ff6kor0c	215	27	68	68	CD
cord-263987-ff6kor0c	215	28	,	,	,
cord-263987-ff6kor0c	215	29	111	111	CD
cord-263987-ff6kor0c	215	30	,	,	,
cord-263987-ff6kor0c	215	31	112	112	CD
cord-263987-ff6kor0c	215	32	]	]	-RRB-
cord-263987-ff6kor0c	215	33	.	.	.
cord-263987-ff6kor0c	216	1	Other	other	JJ
cord-263987-ff6kor0c	216	2	applications	application	NNS
cord-263987-ff6kor0c	216	3	of	of	IN
cord-263987-ff6kor0c	216	4	transducer	transducer	NN
cord-263987-ff6kor0c	216	5	models	model	NNS
cord-263987-ff6kor0c	216	6	in	in	IN
cord-263987-ff6kor0c	216	7	bioinformatics	bioinformatic	NNS
cord-263987-ff6kor0c	216	8	have	have	VBP
cord-263987-ff6kor0c	216	9	included	include	VBN
cord-263987-ff6kor0c	216	10	copy	copy	NN
cord-263987-ff6kor0c	216	11	number	number	NN
cord-263987-ff6kor0c	216	12	variation	variation	NN
cord-263987-ff6kor0c	216	13	in	in	IN
cord-263987-ff6kor0c	216	14	tumors	tumor	NNS
cord-263987-ff6kor0c	216	15	[	[	-LRB-
cord-263987-ff6kor0c	216	16	113	113	CD
cord-263987-ff6kor0c	216	17	]	]	-RRB-
cord-263987-ff6kor0c	216	18	,	,	,
cord-263987-ff6kor0c	216	19	protein	protein	NN
cord-263987-ff6kor0c	216	20	family	family	NN
cord-263987-ff6kor0c	216	21	classification	classification	NN
cord-263987-ff6kor0c	216	22	[	[	-LRB-
cord-263987-ff6kor0c	216	23	114	114	CD
cord-263987-ff6kor0c	216	24	]	]	-RRB-
cord-263987-ff6kor0c	216	25	,	,	,
cord-263987-ff6kor0c	216	26	DNA	dna	NN
cord-263987-ff6kor0c	216	27	-	-	HYPH
cord-263987-ff6kor0c	216	28	protein	protein	NN
cord-263987-ff6kor0c	216	29	alignment	alignment	NN
cord-263987-ff6kor0c	216	30	[	[	-LRB-
cord-263987-ff6kor0c	216	31	115	115	CD
cord-263987-ff6kor0c	216	32	]	]	-RRB-
cord-263987-ff6kor0c	216	33	and	and	CC
cord-263987-ff6kor0c	216	34	error	error	NN
cord-263987-ff6kor0c	216	35	-	-	HYPH
cord-263987-ff6kor0c	216	36	correcting	correct	VBG
cord-263987-ff6kor0c	216	37	codes	code	NNS
cord-263987-ff6kor0c	216	38	for	for	IN
cord-263987-ff6kor0c	216	39	DNA	dna	NN
cord-263987-ff6kor0c	216	40	storage	storage	NN
cord-263987-ff6kor0c	216	41	[	[	-LRB-
cord-263987-ff6kor0c	216	42	116	116	CD
cord-263987-ff6kor0c	216	43	]	]	-RRB-
cord-263987-ff6kor0c	216	44	.	.	.
cord-263987-ff6kor0c	217	1	A	a	DT
cord-263987-ff6kor0c	217	2	finite	finite	JJ
cord-263987-ff6kor0c	217	3	-	-	HYPH
cord-263987-ff6kor0c	217	4	state	state	NN
cord-263987-ff6kor0c	217	5	transducer	transducer	NN
cord-263987-ff6kor0c	217	6	is	be	VBZ
cord-263987-ff6kor0c	217	7	a	a	DT
cord-263987-ff6kor0c	217	8	state	state	NN
cord-263987-ff6kor0c	217	9	machine	machine	NN
cord-263987-ff6kor0c	217	10	that	that	WDT
cord-263987-ff6kor0c	217	11	reads	read	VBZ
cord-263987-ff6kor0c	217	12	an	an	DT
cord-263987-ff6kor0c	217	13	input	input	NN
cord-263987-ff6kor0c	217	14	tape	tape	NN
cord-263987-ff6kor0c	217	15	and	and	CC
cord-263987-ff6kor0c	217	16	writes	write	VBZ
cord-263987-ff6kor0c	217	17	to	to	IN
cord-263987-ff6kor0c	217	18	an	an	DT
cord-263987-ff6kor0c	217	19	output	output	NN
cord-263987-ff6kor0c	217	20	tape	tape	NN
cord-263987-ff6kor0c	217	21	[	[	-LRB-
cord-263987-ff6kor0c	217	22	117	117	CD
cord-263987-ff6kor0c	217	23	]	]	-RRB-
cord-263987-ff6kor0c	217	24	.	.	.
cord-263987-ff6kor0c	218	1	A	a	DT
cord-263987-ff6kor0c	218	2	probabilistically	probabilistically	RB
cord-263987-ff6kor0c	218	3	weighted	weight	VBN
cord-263987-ff6kor0c	218	4	finite	finite	JJ
cord-263987-ff6kor0c	218	5	-	-	HYPH
cord-263987-ff6kor0c	218	6	state	state	NN
cord-263987-ff6kor0c	218	7	transducer	transducer	NN
cord-263987-ff6kor0c	218	8	is	be	VBZ
cord-263987-ff6kor0c	218	9	the	the	DT
cord-263987-ff6kor0c	218	10	same	same	JJ
cord-263987-ff6kor0c	218	11	,	,	,
cord-263987-ff6kor0c	218	12	but	but	CC
cord-263987-ff6kor0c	218	13	its	-PRON-	PRP$
cord-263987-ff6kor0c	218	14	behavior	behavior	NN
cord-263987-ff6kor0c	218	15	is	be	VBZ
cord-263987-ff6kor0c	218	16	stochastic	stochastic	JJ
cord-263987-ff6kor0c	218	17	[	[	-LRB-
cord-263987-ff6kor0c	218	18	110	110	CD
cord-263987-ff6kor0c	218	19	]	]	-RRB-
cord-263987-ff6kor0c	218	20	.	.	.
cord-263987-ff6kor0c	219	1	For	for	IN
cord-263987-ff6kor0c	219	2	the	the	DT
cord-263987-ff6kor0c	219	3	purposes	purpose	NNS
cord-263987-ff6kor0c	219	4	of	of	IN
cord-263987-ff6kor0c	219	5	bioinformatics	bioinformatics	NN
cord-263987-ff6kor0c	219	6	sequence	sequence	NN
cord-263987-ff6kor0c	219	7	analysis	analysis	NN
cord-263987-ff6kor0c	219	8	,	,	,
cord-263987-ff6kor0c	219	9	a	a	DT
cord-263987-ff6kor0c	219	10	transducer	transducer	NN
cord-263987-ff6kor0c	219	11	can	can	MD
cord-263987-ff6kor0c	219	12	be	be	VB
cord-263987-ff6kor0c	219	13	thought	think	VBN
cord-263987-ff6kor0c	219	14	of	of	IN
cord-263987-ff6kor0c	219	15	as	as	IN
cord-263987-ff6kor0c	219	16	being	be	VBG
cord-263987-ff6kor0c	219	17	just	just	RB
cord-263987-ff6kor0c	219	18	like	like	IN
cord-263987-ff6kor0c	219	19	a	a	DT
cord-263987-ff6kor0c	219	20	Pair	pair	NN
cord-263987-ff6kor0c	219	21	HMM	hmm	NN
cord-263987-ff6kor0c	219	22	;	;	:
cord-263987-ff6kor0c	219	23	except	except	IN
cord-263987-ff6kor0c	219	24	where	where	WRB
cord-263987-ff6kor0c	219	25	a	a	DT
cord-263987-ff6kor0c	219	26	Pair	pair	NN
cord-263987-ff6kor0c	219	27	HMM	HMM	NNP
cord-263987-ff6kor0c	219	28	's	's	POS
cord-263987-ff6kor0c	219	29	transition	transition	NN
cord-263987-ff6kor0c	219	30	and	and	CC
cord-263987-ff6kor0c	219	31	emission	emission	NN
cord-263987-ff6kor0c	219	32	probabilities	probability	NNS
cord-263987-ff6kor0c	219	33	have	have	VBP
cord-263987-ff6kor0c	219	34	been	be	VBN
cord-263987-ff6kor0c	219	35	normalized	normalize	VBN
cord-263987-ff6kor0c	219	36	so	so	IN
cord-263987-ff6kor0c	219	37	as	as	IN
cord-263987-ff6kor0c	219	38	to	to	TO
cord-263987-ff6kor0c	219	39	describe	describe	VB
cord-263987-ff6kor0c	219	40	joint	joint	JJ
cord-263987-ff6kor0c	219	41	probabilities	probability	NNS
cord-263987-ff6kor0c	219	42	,	,	,
cord-263987-ff6kor0c	219	43	a	a	DT
cord-263987-ff6kor0c	219	44	transducer	transducer	NN
cord-263987-ff6kor0c	219	45	's	's	POS
cord-263987-ff6kor0c	219	46	probabilities	probability	NNS
cord-263987-ff6kor0c	219	47	are	be	VBP
cord-263987-ff6kor0c	219	48	normalized	normalize	VBN
cord-263987-ff6kor0c	219	49	so	so	IN
cord-263987-ff6kor0c	219	50	as	as	IN
cord-263987-ff6kor0c	219	51	to	to	TO
cord-263987-ff6kor0c	219	52	describe	describe	VB
cord-263987-ff6kor0c	219	53	conditional	conditional	JJ
cord-263987-ff6kor0c	219	54	probabilities	probability	NNS
cord-263987-ff6kor0c	219	55	like	like	IN
cord-263987-ff6kor0c	219	56	the	the	DT
cord-263987-ff6kor0c	219	57	entries	entry	NNS
cord-263987-ff6kor0c	219	58	of	of	IN
cord-263987-ff6kor0c	219	59	matrix	matrix	NN
cord-263987-ff6kor0c	219	60	M(t	M(t	NNS
cord-263987-ff6kor0c	219	61	)	)	-RRB-
cord-263987-ff6kor0c	220	1	(	(	-LRB-
cord-263987-ff6kor0c	220	2	Eq	Eq	NNP
cord-263987-ff6kor0c	220	3	.	.	NNP
cord-263987-ff6kor0c	220	4	2	2	CD
cord-263987-ff6kor0c	220	5	)	)	-RRB-
cord-263987-ff6kor0c	220	6	.	.	.
cord-263987-ff6kor0c	221	1	More	more	RBR
cord-263987-ff6kor0c	221	2	specifically	specifically	RB
cord-263987-ff6kor0c	221	3	,	,	,
cord-263987-ff6kor0c	221	4	if	if	IN
cord-263987-ff6kor0c	221	5	i	i	PRP
cord-263987-ff6kor0c	221	6	and	and	CC
cord-263987-ff6kor0c	221	7	j	j	NNP
cord-263987-ff6kor0c	221	8	are	be	VBP
cord-263987-ff6kor0c	221	9	sequences	sequence	NNS
cord-263987-ff6kor0c	221	10	,	,	,
cord-263987-ff6kor0c	221	11	then	then	RB
cord-263987-ff6kor0c	221	12	one	one	PRP
cord-263987-ff6kor0c	221	13	can	can	MD
cord-263987-ff6kor0c	221	14	define	define	VB
cord-263987-ff6kor0c	221	15	the	the	DT
cord-263987-ff6kor0c	221	16	matrix	matrix	NN
cord-263987-ff6kor0c	221	17	entry	entry	NN
cord-263987-ff6kor0c	222	1	A	a	DT
cord-263987-ff6kor0c	223	1	i	i	PRP
cord-263987-ff6kor0c	223	2	,	,	,
cord-263987-ff6kor0c	223	3	j	j	NNP
cord-263987-ff6kor0c	223	4	to	to	TO
cord-263987-ff6kor0c	223	5	be	be	VB
cord-263987-ff6kor0c	223	6	the	the	DT
cord-263987-ff6kor0c	223	7	Forward	forward	JJ
cord-263987-ff6kor0c	223	8	score	score	NN
cord-263987-ff6kor0c	223	9	for	for	IN
cord-263987-ff6kor0c	223	10	those	those	DT
cord-263987-ff6kor0c	223	11	two	two	CD
cord-263987-ff6kor0c	223	12	sequences	sequence	NNS
cord-263987-ff6kor0c	223	13	using	use	VBG
cord-263987-ff6kor0c	223	14	transducer	transducer	NN
cord-263987-ff6kor0c	223	15	A.	a.	NN
cord-263987-ff6kor0c	224	1	Thus	thus	RB
cord-263987-ff6kor0c	224	2	,	,	,
cord-263987-ff6kor0c	224	3	the	the	DT
cord-263987-ff6kor0c	224	4	transducer	transducer	NN
cord-263987-ff6kor0c	224	5	is	be	VBZ
cord-263987-ff6kor0c	224	6	a	a	DT
cord-263987-ff6kor0c	224	7	compact	compact	JJ
cord-263987-ff6kor0c	224	8	encoding	encoding	NN
cord-263987-ff6kor0c	224	9	for	for	IN
cord-263987-ff6kor0c	224	10	a	a	DT
cord-263987-ff6kor0c	224	11	square	square	JJ
cord-263987-ff6kor0c	224	12	matrix	matrix	NN
cord-263987-ff6kor0c	224	13	of	of	IN
cord-263987-ff6kor0c	224	14	countably	countably	DT
cord-263987-ff6kor0c	224	15	infinite	infinite	JJ
cord-263987-ff6kor0c	224	16	rank	rank	NN
cord-263987-ff6kor0c	224	17	,	,	,
cord-263987-ff6kor0c	224	18	indexed	index	VBN
cord-263987-ff6kor0c	224	19	by	by	IN
cord-263987-ff6kor0c	224	20	sequence	sequence	NN
cord-263987-ff6kor0c	224	21	states	state	NNS
cord-263987-ff6kor0c	224	22	(	(	-LRB-
cord-263987-ff6kor0c	224	23	rather	rather	RB
cord-263987-ff6kor0c	224	24	than	than	IN
cord-263987-ff6kor0c	224	25	nucleotide	nucleotide	JJ
cord-263987-ff6kor0c	224	26	or	or	CC
cord-263987-ff6kor0c	224	27	amino	amino	NN
cord-263987-ff6kor0c	224	28	acid	acid	NN
cord-263987-ff6kor0c	224	29	states	state	NNS
cord-263987-ff6kor0c	224	30	)	)	-RRB-
cord-263987-ff6kor0c	224	31	.	.	.
cord-263987-ff6kor0c	225	1	The	the	DT
cord-263987-ff6kor0c	225	2	utility	utility	NN
cord-263987-ff6kor0c	225	3	of	of	IN
cord-263987-ff6kor0c	225	4	transducers	transducer	NNS
cord-263987-ff6kor0c	225	5	arises	arise	VBZ
cord-263987-ff6kor0c	225	6	since	since	IN
cord-263987-ff6kor0c	225	7	for	for	IN
cord-263987-ff6kor0c	225	8	many	many	JJ
cord-263987-ff6kor0c	225	9	purposes	purpose	NNS
cord-263987-ff6kor0c	225	10	they	-PRON-	PRP
cord-263987-ff6kor0c	225	11	can	can	MD
cord-263987-ff6kor0c	225	12	be	be	VB
cord-263987-ff6kor0c	225	13	manipulated	manipulate	VBN
cord-263987-ff6kor0c	225	14	analogously	analogously	RB
cord-263987-ff6kor0c	225	15	to	to	IN
cord-263987-ff6kor0c	225	16	matrices	matrix	NNS
cord-263987-ff6kor0c	225	17	,	,	,
cord-263987-ff6kor0c	225	18	while	while	IN
cord-263987-ff6kor0c	225	19	being	be	VBG
cord-263987-ff6kor0c	225	20	more	more	RBR
cord-263987-ff6kor0c	225	21	compact	compact	JJ
cord-263987-ff6kor0c	225	22	than	than	IN
cord-263987-ff6kor0c	225	23	the	the	DT
cord-263987-ff6kor0c	225	24	corresponding	correspond	VBG
cord-263987-ff6kor0c	225	25	matrix	matrix	NN
cord-263987-ff6kor0c	225	26	(	(	-LRB-
cord-263987-ff6kor0c	225	27	as	as	IN
cord-263987-ff6kor0c	225	28	noted	note	VBN
cord-263987-ff6kor0c	225	29	above	above	RB
cord-263987-ff6kor0c	225	30	,	,	,
cord-263987-ff6kor0c	225	31	matrices	matrix	NNS
cord-263987-ff6kor0c	225	32	describing	describe	VBG
cord-263987-ff6kor0c	225	33	evolution	evolution	NN
cord-263987-ff6kor0c	225	34	of	of	IN
cord-263987-ff6kor0c	225	35	arbitrary	arbitrary	JJ
cord-263987-ff6kor0c	225	36	-	-	HYPH
cord-263987-ff6kor0c	225	37	length	length	NN
cord-263987-ff6kor0c	225	38	sequences	sequence	NNS
cord-263987-ff6kor0c	225	39	are	be	VBP
cord-263987-ff6kor0c	225	40	impractically	impractically	RB
cord-263987-ff6kor0c	225	41	-	-	:
cord-263987-ff6kor0c	225	42	or	or	CC
cord-263987-ff6kor0c	225	43	even	even	RB
cord-263987-ff6kor0c	225	44	infinitely	infinitely	RB
cord-263987-ff6kor0c	225	45	-	-	HYPH
cord-263987-ff6kor0c	225	46	large	large	JJ
cord-263987-ff6kor0c	225	47	)	)	-RRB-
cord-263987-ff6kor0c	225	48	.	.	.
cord-263987-ff6kor0c	226	1	If	if	IN
cord-263987-ff6kor0c	226	2	A	a	NN
cord-263987-ff6kor0c	226	3	and	and	CC
cord-263987-ff6kor0c	226	4	B	b	NN
cord-263987-ff6kor0c	226	5	are	be	VBP
cord-263987-ff6kor0c	226	6	finite	finite	JJ
cord-263987-ff6kor0c	226	7	transducers	transducer	NNS
cord-263987-ff6kor0c	226	8	encoding	encode	VBG
cord-263987-ff6kor0c	226	9	(	(	-LRB-
cord-263987-ff6kor0c	226	10	potentially	potentially	RB
cord-263987-ff6kor0c	226	11	infinite	infinite	JJ
cord-263987-ff6kor0c	226	12	)	)	-RRB-
cord-263987-ff6kor0c	226	13	matrices	matrix	NNS
cord-263987-ff6kor0c	226	14	A	a	NN
cord-263987-ff6kor0c	226	15	and	and	CC
cord-263987-ff6kor0c	226	16	B	b	NN
cord-263987-ff6kor0c	226	17	,	,	,
cord-263987-ff6kor0c	226	18	then	then	RB
cord-263987-ff6kor0c	226	19	there	there	EX
cord-263987-ff6kor0c	226	20	is	be	VBZ
cord-263987-ff6kor0c	226	21	a	a	DT
cord-263987-ff6kor0c	226	22	well	well	RB
cord-263987-ff6kor0c	226	23	-	-	HYPH
cord-263987-ff6kor0c	226	24	defined	define	VBN
cord-263987-ff6kor0c	226	25	operation	operation	NN
cord-263987-ff6kor0c	226	26	called	call	VBN
cord-263987-ff6kor0c	226	27	transducer	transducer	NN
cord-263987-ff6kor0c	226	28	composition	composition	NN
cord-263987-ff6kor0c	226	29	yielding	yield	VBG
cord-263987-ff6kor0c	226	30	a	a	DT
cord-263987-ff6kor0c	226	31	finite	finite	JJ
cord-263987-ff6kor0c	226	32	transducer	transducer	NN
cord-263987-ff6kor0c	226	33	AB	AB	NNP
cord-263987-ff6kor0c	226	34	that	that	WDT
cord-263987-ff6kor0c	226	35	represents	represent	VBZ
cord-263987-ff6kor0c	226	36	the	the	DT
cord-263987-ff6kor0c	226	37	matrix	matrix	NN
cord-263987-ff6kor0c	226	38	product	product	NN
cord-263987-ff6kor0c	226	39	AB	AB	NNP
cord-263987-ff6kor0c	226	40	.	.	.
cord-263987-ff6kor0c	227	1	There	there	EX
cord-263987-ff6kor0c	227	2	are	be	VBP
cord-263987-ff6kor0c	227	3	other	other	JJ
cord-263987-ff6kor0c	227	4	well	well	RB
cord-263987-ff6kor0c	227	5	-	-	HYPH
cord-263987-ff6kor0c	227	6	defined	define	VBN
cord-263987-ff6kor0c	227	7	transducer	transducer	NN
cord-263987-ff6kor0c	227	8	operations	operation	NNS
cord-263987-ff6kor0c	227	9	corresponding	correspond	VBG
cord-263987-ff6kor0c	227	10	to	to	IN
cord-263987-ff6kor0c	227	11	the	the	DT
cord-263987-ff6kor0c	227	12	various	various	JJ
cord-263987-ff6kor0c	227	13	other	other	JJ
cord-263987-ff6kor0c	227	14	linear	linear	JJ
cord-263987-ff6kor0c	227	15	algebra	algebra	NN
cord-263987-ff6kor0c	227	16	operations	operation	NNS
cord-263987-ff6kor0c	227	17	used	use	VBN
cord-263987-ff6kor0c	227	18	in	in	IN
cord-263987-ff6kor0c	227	19	this	this	DT
cord-263987-ff6kor0c	227	20	paper	paper	NN
cord-263987-ff6kor0c	227	21	:	:	:
cord-263987-ff6kor0c	227	22	the	the	DT
cord-263987-ff6kor0c	227	23	Hadamard	Hadamard	NNP
cord-263987-ff6kor0c	227	24	product	product	NN
cord-263987-ff6kor0c	227	25	(	(	-LRB-
cord-263987-ff6kor0c	227	26	•	•	NNP
cord-263987-ff6kor0c	227	27	)	)	-RRB-
cord-263987-ff6kor0c	227	28	corresponds	correspond	VBZ
cord-263987-ff6kor0c	227	29	to	to	IN
cord-263987-ff6kor0c	227	30	transducer	transducer	NN
cord-263987-ff6kor0c	227	31	intersection	intersection	NN
cord-263987-ff6kor0c	227	32	,	,	,
cord-263987-ff6kor0c	228	1	the	the	DT
cord-263987-ff6kor0c	228	2	Kronecker	Kronecker	NNP
cord-263987-ff6kor0c	228	3	product	product	NN
cord-263987-ff6kor0c	228	4	(	(	-LRB-
cord-263987-ff6kor0c	228	5	⊗	⊗	NNP
cord-263987-ff6kor0c	228	6	)	)	-RRB-
cord-263987-ff6kor0c	228	7	corresponds	correspond	VBZ
cord-263987-ff6kor0c	228	8	to	to	IN
cord-263987-ff6kor0c	228	9	transducer	transducer	NN
cord-263987-ff6kor0c	228	10	concatenation	concatenation	NN
cord-263987-ff6kor0c	228	11	,	,	,
cord-263987-ff6kor0c	228	12	and	and	CC
cord-263987-ff6kor0c	228	13	the	the	DT
cord-263987-ff6kor0c	228	14	scalar	scalar	JJ
cord-263987-ff6kor0c	228	15	product	product	NN
cord-263987-ff6kor0c	228	16	(	(	-LRB-
cord-263987-ff6kor0c	228	17	·	·	NFP
cord-263987-ff6kor0c	228	18	)	)	-RRB-
cord-263987-ff6kor0c	228	19	and	and	CC
cord-263987-ff6kor0c	228	20	the	the	DT
cord-263987-ff6kor0c	228	21	unit	unit	NN
cord-263987-ff6kor0c	228	22	vector	vector	NN
cord-263987-ff6kor0c	228	23	(	(	-LRB-
cord-263987-ff6kor0c	228	24	)	)	-RRB-
cord-263987-ff6kor0c	228	25	can	can	MD
cord-263987-ff6kor0c	228	26	also	also	RB
cord-263987-ff6kor0c	228	27	readily	readily	RB
cord-263987-ff6kor0c	228	28	be	be	VB
cord-263987-ff6kor0c	228	29	constructed	construct	VBN
cord-263987-ff6kor0c	228	30	using	use	VBG
cord-263987-ff6kor0c	228	31	transducers	transducer	NNS
cord-263987-ff6kor0c	228	32	.	.	.
cord-263987-ff6kor0c	229	1	Consequently	consequently	RB
cord-263987-ff6kor0c	229	2	,	,	,
cord-263987-ff6kor0c	229	3	Eq	Eq	NNP
cord-263987-ff6kor0c	229	4	.	.	NNP
cord-263987-ff6kor0c	229	5	4	4	CD
cord-263987-ff6kor0c	229	6	can	can	MD
cord-263987-ff6kor0c	229	7	be	be	VB
cord-263987-ff6kor0c	229	8	interpreted	interpret	VBN
cord-263987-ff6kor0c	229	9	directly	directly	RB
cord-263987-ff6kor0c	229	10	in	in	IN
cord-263987-ff6kor0c	229	11	terms	term	NNS
cord-263987-ff6kor0c	229	12	of	of	IN
cord-263987-ff6kor0c	229	13	transducers	transducer	NNS
cord-263987-ff6kor0c	229	14	[	[	-LRB-
cord-263987-ff6kor0c	229	15	67	67	CD
cord-263987-ff6kor0c	229	16	,	,	,
cord-263987-ff6kor0c	229	17	68	68	CD
cord-263987-ff6kor0c	229	18	,	,	,
cord-263987-ff6kor0c	229	19	82	82	CD
cord-263987-ff6kor0c	229	20	]	]	-RRB-
cord-263987-ff6kor0c	229	21	.	.	.
cord-263987-ff6kor0c	230	1	This	this	DT
cord-263987-ff6kor0c	230	2	has	have	VBZ
cord-263987-ff6kor0c	230	3	several	several	JJ
cord-263987-ff6kor0c	230	4	benefits	benefit	NNS
cord-263987-ff6kor0c	230	5	.	.	.
cord-263987-ff6kor0c	231	1	One	one	CD
cord-263987-ff6kor0c	231	2	is	be	VBZ
cord-263987-ff6kor0c	231	3	theoretical	theoretical	JJ
cord-263987-ff6kor0c	231	4	unification	unification	NN
cord-263987-ff6kor0c	231	5	:	:	:
cord-263987-ff6kor0c	231	6	Eq	Eq	NNP
cord-263987-ff6kor0c	231	7	.	.	.
cord-263987-ff6kor0c	232	1	4	4	LS
cord-263987-ff6kor0c	232	2	,	,	,
cord-263987-ff6kor0c	232	3	using	use	VBG
cord-263987-ff6kor0c	232	4	the	the	DT
cord-263987-ff6kor0c	232	5	above	above	JJ
cord-263987-ff6kor0c	232	6	linear	linear	JJ
cord-263987-ff6kor0c	232	7	algebra	algebra	NN
cord-263987-ff6kor0c	232	8	interpretation	interpretation	NN
cord-263987-ff6kor0c	232	9	of	of	IN
cord-263987-ff6kor0c	232	10	transducer	transducer	NN
cord-263987-ff6kor0c	232	11	manipulations	manipulation	NNS
cord-263987-ff6kor0c	232	12	,	,	,
cord-263987-ff6kor0c	232	13	turns	turn	VBZ
cord-263987-ff6kor0c	232	14	out	out	RP
cord-263987-ff6kor0c	232	15	to	to	TO
cord-263987-ff6kor0c	232	16	be	be	VB
cord-263987-ff6kor0c	232	17	very	very	RB
cord-263987-ff6kor0c	232	18	similar	similar	JJ
cord-263987-ff6kor0c	232	19	to	to	IN
cord-263987-ff6kor0c	232	20	Sankoff	Sankoff	NNP
cord-263987-ff6kor0c	232	21	's	's	POS
cord-263987-ff6kor0c	232	22	algorithm	algorithm	NN
cord-263987-ff6kor0c	232	23	for	for	IN
cord-263987-ff6kor0c	232	24	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	232	25	multiple	multiple	JJ
cord-263987-ff6kor0c	232	26	alignment	alignment	NN
cord-263987-ff6kor0c	232	27	[	[	-LRB-
cord-263987-ff6kor0c	232	28	118	118	CD
cord-263987-ff6kor0c	232	29	]	]	-RRB-
cord-263987-ff6kor0c	232	30	.	.	.
cord-263987-ff6kor0c	233	1	Thus	thus	RB
cord-263987-ff6kor0c	233	2	is	be	VBZ
cord-263987-ff6kor0c	233	3	a	a	DT
cord-263987-ff6kor0c	233	4	famous	famous	JJ
cord-263987-ff6kor0c	233	5	algorithm	algorithm	NN
cord-263987-ff6kor0c	233	6	in	in	IN
cord-263987-ff6kor0c	233	7	bioinformatics	bioinformatic	NNS
cord-263987-ff6kor0c	233	8	unified	unify	VBN
cord-263987-ff6kor0c	233	9	with	with	IN
cord-263987-ff6kor0c	233	10	a	a	DT
cord-263987-ff6kor0c	233	11	famous	famous	JJ
cord-263987-ff6kor0c	233	12	algorithm	algorithm	NN
cord-263987-ff6kor0c	233	13	in	in	IN
cord-263987-ff6kor0c	233	14	likelihood	likelihood	NN
cord-263987-ff6kor0c	233	15	phylogenetics	phylogenetic	NNS
cord-263987-ff6kor0c	233	16	by	by	IN
cord-263987-ff6kor0c	233	17	using	use	VBG
cord-263987-ff6kor0c	233	18	a	a	DT
cord-263987-ff6kor0c	233	19	tool	tool	NN
cord-263987-ff6kor0c	233	20	from	from	IN
cord-263987-ff6kor0c	233	21	computational	computational	JJ
cord-263987-ff6kor0c	233	22	linguistics	linguistics	NN
cord-263987-ff6kor0c	233	23	.	.	.
cord-263987-ff6kor0c	234	1	(	(	-LRB-
cord-263987-ff6kor0c	234	2	This	this	DT
cord-263987-ff6kor0c	234	3	excludes	exclude	VBZ
cord-263987-ff6kor0c	234	4	the	the	DT
cord-263987-ff6kor0c	234	5	RNA	RNA	NNP
cord-263987-ff6kor0c	234	6	structure	structure	NN
cord-263987-ff6kor0c	234	7	-	-	HYPH
cord-263987-ff6kor0c	234	8	prediction	prediction	NN
cord-263987-ff6kor0c	234	9	component	component	NN
cord-263987-ff6kor0c	234	10	of	of	IN
cord-263987-ff6kor0c	234	11	Sankoff	Sankoff	NNP
cord-263987-ff6kor0c	234	12	's	's	POS
cord-263987-ff6kor0c	234	13	algorithm	algorithm	NN
cord-263987-ff6kor0c	234	14	;	;	:
cord-263987-ff6kor0c	234	15	that	that	DT
cord-263987-ff6kor0c	234	16	can	can	MD
cord-263987-ff6kor0c	234	17	,	,	,
cord-263987-ff6kor0c	234	18	however	however	RB
cord-263987-ff6kor0c	234	19	,	,	,
cord-263987-ff6kor0c	234	20	be	be	VB
cord-263987-ff6kor0c	234	21	included	include	VBN
cord-263987-ff6kor0c	234	22	by	by	IN
cord-263987-ff6kor0c	234	23	extending	extend	VBG
cord-263987-ff6kor0c	234	24	the	the	DT
cord-263987-ff6kor0c	234	25	transducer	transducer	NN
cord-263987-ff6kor0c	234	26	framework	framework	NN
cord-263987-ff6kor0c	234	27	to	to	IN
cord-263987-ff6kor0c	234	28	pushdown	pushdown	JJ
cord-263987-ff6kor0c	234	29	automata	automaton	NNS
cord-263987-ff6kor0c	234	30	[	[	-LRB-
cord-263987-ff6kor0c	234	31	119	119	CD
cord-263987-ff6kor0c	234	32	]	]	-RRB-
cord-263987-ff6kor0c	234	33	.	.	.
cord-263987-ff6kor0c	234	34	)	)	-RRB-
cord-263987-ff6kor0c	235	1	Practically	practically	RB
cord-263987-ff6kor0c	235	2	,	,	,
cord-263987-ff6kor0c	235	3	the	the	DT
cord-263987-ff6kor0c	235	4	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	235	5	transducer	transducer	NN
cord-263987-ff6kor0c	235	6	can	can	MD
cord-263987-ff6kor0c	235	7	be	be	VB
cord-263987-ff6kor0c	235	8	used	use	VBN
cord-263987-ff6kor0c	235	9	for	for	IN
cord-263987-ff6kor0c	235	10	alignment	alignment	NN
cord-263987-ff6kor0c	235	11	[	[	-LRB-
cord-263987-ff6kor0c	235	12	79	79	CD
cord-263987-ff6kor0c	235	13	,	,	,
cord-263987-ff6kor0c	235	14	81	81	CD
cord-263987-ff6kor0c	235	15	]	]	-RRB-
cord-263987-ff6kor0c	235	16	,	,	,
cord-263987-ff6kor0c	235	17	parameter	parameter	NN
cord-263987-ff6kor0c	235	18	estimation	estimation	NN
cord-263987-ff6kor0c	235	19	[	[	-LRB-
cord-263987-ff6kor0c	235	20	104	104	CD
cord-263987-ff6kor0c	235	21	]	]	-RRB-
cord-263987-ff6kor0c	235	22	,	,	,
cord-263987-ff6kor0c	235	23	and	and	CC
cord-263987-ff6kor0c	235	24	ancestral	ancestral	JJ
cord-263987-ff6kor0c	235	25	reconstruction	reconstruction	NN
cord-263987-ff6kor0c	235	26	[	[	-LRB-
cord-263987-ff6kor0c	235	27	67	67	CD
cord-263987-ff6kor0c	235	28	]	]	-RRB-
cord-263987-ff6kor0c	235	29	,	,	,
cord-263987-ff6kor0c	235	30	with	with	IN
cord-263987-ff6kor0c	235	31	promising	promising	JJ
cord-263987-ff6kor0c	235	32	results	result	NNS
cord-263987-ff6kor0c	235	33	for	for	IN
cord-263987-ff6kor0c	235	34	improved	improved	JJ
cord-263987-ff6kor0c	235	35	accuracy	accuracy	NN
cord-263987-ff6kor0c	235	36	in	in	IN
cord-263987-ff6kor0c	235	37	multiple	multiple	JJ
cord-263987-ff6kor0c	235	38	sequence	sequence	NN
cord-263987-ff6kor0c	235	39	alignment	alignment	NN
cord-263987-ff6kor0c	235	40	[	[	-LRB-
cord-263987-ff6kor0c	235	41	112	112	CD
cord-263987-ff6kor0c	235	42	]	]	-RRB-
cord-263987-ff6kor0c	235	43	.	.	.
cord-263987-ff6kor0c	236	1	More	more	RBR
cord-263987-ff6kor0c	236	2	broadly	broadly	RB
cord-263987-ff6kor0c	236	3	,	,	,
cord-263987-ff6kor0c	236	4	one	one	PRP
cord-263987-ff6kor0c	236	5	can	can	MD
cord-263987-ff6kor0c	236	6	think	think	VB
cord-263987-ff6kor0c	236	7	of	of	IN
cord-263987-ff6kor0c	236	8	the	the	DT
cord-263987-ff6kor0c	236	9	transducer	transducer	NN
cord-263987-ff6kor0c	236	10	as	as	IN
cord-263987-ff6kor0c	236	11	being	be	VBG
cord-263987-ff6kor0c	236	12	in	in	IN
cord-263987-ff6kor0c	236	13	a	a	DT
cord-263987-ff6kor0c	236	14	family	family	NN
cord-263987-ff6kor0c	236	15	of	of	IN
cord-263987-ff6kor0c	236	16	methods	method	NNS
cord-263987-ff6kor0c	236	17	that	that	WDT
cord-263987-ff6kor0c	236	18	combine	combine	VBP
cord-263987-ff6kor0c	236	19	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	236	20	trees	tree	NNS
cord-263987-ff6kor0c	236	21	(	(	-LRB-
cord-263987-ff6kor0c	236	22	modeling	model	VBG
cord-263987-ff6kor0c	236	23	the	the	DT
cord-263987-ff6kor0c	236	24	temporal	temporal	JJ
cord-263987-ff6kor0c	236	25	structure	structure	NN
cord-263987-ff6kor0c	236	26	of	of	IN
cord-263987-ff6kor0c	236	27	evolution	evolution	NN
cord-263987-ff6kor0c	236	28	)	)	-RRB-
cord-263987-ff6kor0c	236	29	with	with	IN
cord-263987-ff6kor0c	236	30	automata	automata	NN
cord-263987-ff6kor0c	236	31	theory	theory	NN
cord-263987-ff6kor0c	236	32	,	,	,
cord-263987-ff6kor0c	236	33	grammars	grammar	NNS
cord-263987-ff6kor0c	236	34	,	,	,
cord-263987-ff6kor0c	236	35	and	and	CC
cord-263987-ff6kor0c	236	36	dynamic	dynamic	JJ
cord-263987-ff6kor0c	236	37	programming	programming	NN
cord-263987-ff6kor0c	236	38	on	on	IN
cord-263987-ff6kor0c	236	39	sequences	sequence	NNS
cord-263987-ff6kor0c	236	40	(	(	-LRB-
cord-263987-ff6kor0c	236	41	modeling	model	VBG
cord-263987-ff6kor0c	236	42	the	the	DT
cord-263987-ff6kor0c	236	43	spatial	spatial	JJ
cord-263987-ff6kor0c	236	44	structure	structure	NN
cord-263987-ff6kor0c	236	45	of	of	IN
cord-263987-ff6kor0c	236	46	evolution	evolution	NN
cord-263987-ff6kor0c	236	47	)	)	-RRB-
cord-263987-ff6kor0c	236	48	.	.	.
cord-263987-ff6kor0c	237	1	The	the	DT
cord-263987-ff6kor0c	237	2	TKF	TKF	NNP
cord-263987-ff6kor0c	237	3	Structure	Structure	NNP
cord-263987-ff6kor0c	237	4	Tree	Tree	NNP
cord-263987-ff6kor0c	237	5	,	,	,
cord-263987-ff6kor0c	237	6	mentioned	mention	VBN
cord-263987-ff6kor0c	237	7	above	above	RB
cord-263987-ff6kor0c	237	8	,	,	,
cord-263987-ff6kor0c	237	9	is	be	VBZ
cord-263987-ff6kor0c	237	10	in	in	IN
cord-263987-ff6kor0c	237	11	this	this	DT
cord-263987-ff6kor0c	237	12	family	family	NN
cord-263987-ff6kor0c	237	13	too	too	RB
cord-263987-ff6kor0c	237	14	:	:	:
cord-263987-ff6kor0c	237	15	it	-PRON-	PRP
cord-263987-ff6kor0c	237	16	can	can	MD
cord-263987-ff6kor0c	237	17	be	be	VB
cord-263987-ff6kor0c	237	18	viewed	view	VBN
cord-263987-ff6kor0c	237	19	as	as	IN
cord-263987-ff6kor0c	237	20	a	a	DT
cord-263987-ff6kor0c	237	21	context	context	NN
cord-263987-ff6kor0c	237	22	-	-	HYPH
cord-263987-ff6kor0c	237	23	free	free	JJ
cord-263987-ff6kor0c	237	24	grammar	grammar	NN
cord-263987-ff6kor0c	237	25	,	,	,
cord-263987-ff6kor0c	237	26	or	or	CC
cord-263987-ff6kor0c	237	27	as	as	IN
cord-263987-ff6kor0c	237	28	a	a	DT
cord-263987-ff6kor0c	237	29	transducer	transducer	NN
cord-263987-ff6kor0c	237	30	with	with	IN
cord-263987-ff6kor0c	237	31	a	a	DT
cord-263987-ff6kor0c	237	32	pushdown	pushdown	NN
cord-263987-ff6kor0c	237	33	stack	stack	NN
cord-263987-ff6kor0c	237	34	[	[	-LRB-
cord-263987-ff6kor0c	237	35	75	75	CD
cord-263987-ff6kor0c	237	36	]	]	-RRB-
cord-263987-ff6kor0c	237	37	.	.	.
cord-263987-ff6kor0c	238	1	The	the	DT
cord-263987-ff6kor0c	238	2	HMM	HMM	NNP
cord-263987-ff6kor0c	238	3	-	-	HYPH
cord-263987-ff6kor0c	238	4	like	like	JJ
cord-263987-ff6kor0c	238	5	nature	nature	NN
cord-263987-ff6kor0c	238	6	of	of	IN
cord-263987-ff6kor0c	238	7	TKF91	TKF91	NNP
cord-263987-ff6kor0c	238	8	,	,	,
cord-263987-ff6kor0c	238	9	and	and	CC
cord-263987-ff6kor0c	238	10	the	the	DT
cord-263987-ff6kor0c	238	11	ubiquity	ubiquity	NN
cord-263987-ff6kor0c	238	12	of	of	IN
cord-263987-ff6kor0c	238	13	HMMs	HMMs	NNP
cord-263987-ff6kor0c	238	14	and	and	CC
cord-263987-ff6kor0c	238	15	dynamic	dynamic	JJ
cord-263987-ff6kor0c	238	16	programming	programming	NN
cord-263987-ff6kor0c	238	17	in	in	IN
cord-263987-ff6kor0c	238	18	sequence	sequence	NN
cord-263987-ff6kor0c	238	19	analysis	analysis	NN
cord-263987-ff6kor0c	238	20	,	,	,
cord-263987-ff6kor0c	238	21	has	have	VBZ
cord-263987-ff6kor0c	238	22	motivated	motivate	VBN
cord-263987-ff6kor0c	238	23	numerous	numerous	JJ
cord-263987-ff6kor0c	238	24	approaches	approach	NNS
cord-263987-ff6kor0c	238	25	to	to	TO
cord-263987-ff6kor0c	238	26	indel	indel	NN
cord-263987-ff6kor0c	238	27	analysis	analysis	NN
cord-263987-ff6kor0c	238	28	based	base	VBN
cord-263987-ff6kor0c	238	29	on	on	IN
cord-263987-ff6kor0c	238	30	Pair	Pair	NNP
cord-263987-ff6kor0c	238	31	HMMs	HMMs	NNPS
cord-263987-ff6kor0c	238	32	[	[	-LRB-
cord-263987-ff6kor0c	238	33	56	56	CD
cord-263987-ff6kor0c	238	34	,	,	,
cord-263987-ff6kor0c	238	35	71	71	CD
cord-263987-ff6kor0c	238	36	,	,	,
cord-263987-ff6kor0c	238	37	74	74	CD
cord-263987-ff6kor0c	238	38	,	,	,
cord-263987-ff6kor0c	238	39	78	78	CD
cord-263987-ff6kor0c	238	40	,	,	,
cord-263987-ff6kor0c	238	41	120	120	CD
cord-263987-ff6kor0c	238	42	]	]	-RRB-
cord-263987-ff6kor0c	238	43	,	,	,
cord-263987-ff6kor0c	238	44	as	as	RB
cord-263987-ff6kor0c	238	45	well	well	RB
cord-263987-ff6kor0c	238	46	as	as	IN
cord-263987-ff6kor0c	238	47	many	many	JJ
cord-263987-ff6kor0c	238	48	other	other	JJ
cord-263987-ff6kor0c	238	49	applications	application	NNS
cord-263987-ff6kor0c	238	50	of	of	IN
cord-263987-ff6kor0c	238	51	phylogenetic	phylogenetic	NN
cord-263987-ff6kor0c	238	52	HMMs	HMMs	NNPS
cord-263987-ff6kor0c	238	53	[	[	-LRB-
cord-263987-ff6kor0c	238	54	6	6	CD
cord-263987-ff6kor0c	238	55	,	,	,
cord-263987-ff6kor0c	238	56	7	7	CD
cord-263987-ff6kor0c	238	57	,	,	,
cord-263987-ff6kor0c	238	58	12	12	CD
cord-263987-ff6kor0c	238	59	,	,	,
cord-263987-ff6kor0c	238	60	121	121	CD
cord-263987-ff6kor0c	238	61	,	,	,
cord-263987-ff6kor0c	238	62	122	122	CD
cord-263987-ff6kor0c	238	63	]	]	-RRB-
cord-263987-ff6kor0c	238	64	and	and	CC
cord-263987-ff6kor0c	238	65	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	238	66	grammars	grammar	NNS
cord-263987-ff6kor0c	238	67	[	[	-LRB-
cord-263987-ff6kor0c	238	68	8	8	CD
cord-263987-ff6kor0c	238	69	,	,	,
cord-263987-ff6kor0c	238	70	10	10	CD
cord-263987-ff6kor0c	238	71	,	,	,
cord-263987-ff6kor0c	238	72	40	40	CD
cord-263987-ff6kor0c	238	73	,	,	,
cord-263987-ff6kor0c	238	74	60	60	CD
cord-263987-ff6kor0c	238	75	,	,	,
cord-263987-ff6kor0c	238	76	123	123	CD
cord-263987-ff6kor0c	238	77	,	,	,
cord-263987-ff6kor0c	238	78	124	124	CD
cord-263987-ff6kor0c	238	79	]	]	-RRB-
cord-263987-ff6kor0c	238	80	.	.	.
cord-263987-ff6kor0c	239	1	In	in	IN
cord-263987-ff6kor0c	239	2	most	most	JJS
cord-263987-ff6kor0c	239	3	of	of	IN
cord-263987-ff6kor0c	239	4	these	these	DT
cord-263987-ff6kor0c	239	5	models	model	NNS
cord-263987-ff6kor0c	239	6	,	,	,
cord-263987-ff6kor0c	239	7	an	an	DT
cord-263987-ff6kor0c	239	8	alignment	alignment	NN
cord-263987-ff6kor0c	239	9	is	be	VBZ
cord-263987-ff6kor0c	239	10	assumed	assume	VBN
cord-263987-ff6kor0c	239	11	fixed	fix	VBN
cord-263987-ff6kor0c	239	12	and	and	CC
cord-263987-ff6kor0c	239	13	the	the	DT
cord-263987-ff6kor0c	239	14	HMM	HMM	NNP
cord-263987-ff6kor0c	239	15	or	or	CC
cord-263987-ff6kor0c	239	16	grammar	grammar	NN
cord-263987-ff6kor0c	239	17	used	use	VBN
cord-263987-ff6kor0c	239	18	to	to	TO
cord-263987-ff6kor0c	239	19	partition	partition	VB
cord-263987-ff6kor0c	239	20	it	-PRON-	PRP
cord-263987-ff6kor0c	239	21	;	;	:
cord-263987-ff6kor0c	239	22	however	however	RB
cord-263987-ff6kor0c	239	23	,	,	,
cord-263987-ff6kor0c	239	24	in	in	IN
cord-263987-ff6kor0c	239	25	principle	principle	NN
cord-263987-ff6kor0c	239	26	,	,	,
cord-263987-ff6kor0c	239	27	one	one	PRP
cord-263987-ff6kor0c	239	28	can	can	MD
cord-263987-ff6kor0c	239	29	combine	combine	VB
cord-263987-ff6kor0c	239	30	the	the	DT
cord-263987-ff6kor0c	239	31	ability	ability	NN
cord-263987-ff6kor0c	239	32	of	of	IN
cord-263987-ff6kor0c	239	33	HMMs	HMMs	NNP
cord-263987-ff6kor0c	239	34	/	/	,
cord-263987-ff6kor0c	239	35	grammars	grammar	NNS
cord-263987-ff6kor0c	239	36	to	to	TO
cord-263987-ff6kor0c	239	37	model	model	VB
cord-263987-ff6kor0c	239	38	indels	indel	NNS
cord-263987-ff6kor0c	239	39	(	(	-LRB-
cord-263987-ff6kor0c	239	40	and	and	CC
cord-263987-ff6kor0c	239	41	thus	thus	RB
cord-263987-ff6kor0c	239	42	impute	impute	VB
cord-263987-ff6kor0c	239	43	alignments	alignment	NNS
cord-263987-ff6kor0c	239	44	)	)	-RRB-
cord-263987-ff6kor0c	239	45	with	with	IN
cord-263987-ff6kor0c	239	46	the	the	DT
cord-263987-ff6kor0c	239	47	ability	ability	NN
cord-263987-ff6kor0c	239	48	to	to	TO
cord-263987-ff6kor0c	239	49	partition	partition	VB
cord-263987-ff6kor0c	239	50	sequences	sequence	NNS
cord-263987-ff6kor0c	239	51	into	into	IN
cord-263987-ff6kor0c	239	52	differently	differently	RB
cord-263987-ff6kor0c	239	53	evolving	evolve	VBG
cord-263987-ff6kor0c	239	54	regions	region	NNS
cord-263987-ff6kor0c	239	55	.	.	.
cord-263987-ff6kor0c	240	1	The	the	DT
cord-263987-ff6kor0c	240	2	promise	promise	NN
cord-263987-ff6kor0c	240	3	of	of	IN
cord-263987-ff6kor0c	240	4	using	use	VBG
cord-263987-ff6kor0c	240	5	continuous	continuous	JJ
cord-263987-ff6kor0c	240	6	-	-	HYPH
cord-263987-ff6kor0c	240	7	time	time	NN
cord-263987-ff6kor0c	240	8	Markov	Markov	NNP
cord-263987-ff6kor0c	240	9	chains	chain	NNS
cord-263987-ff6kor0c	240	10	to	to	TO
cord-263987-ff6kor0c	240	11	model	model	VB
cord-263987-ff6kor0c	240	12	indels	indel	NNS
cord-263987-ff6kor0c	240	13	has	have	VBZ
cord-263987-ff6kor0c	240	14	been	be	VBN
cord-263987-ff6kor0c	240	15	partially	partially	RB
cord-263987-ff6kor0c	240	16	realized	realize	VBN
cord-263987-ff6kor0c	240	17	by	by	IN
cord-263987-ff6kor0c	240	18	automatatheoretic	automatatheoretic	JJ
cord-263987-ff6kor0c	240	19	approaches	approach	NNS
cord-263987-ff6kor0c	240	20	based	base	VBN
cord-263987-ff6kor0c	240	21	on	on	IN
cord-263987-ff6kor0c	240	22	transducers	transducer	NNS
cord-263987-ff6kor0c	240	23	and	and	CC
cord-263987-ff6kor0c	240	24	HMMs	HMMs	NNP
cord-263987-ff6kor0c	240	25	.	.	.
cord-263987-ff6kor0c	241	1	Recent	recent	JJ
cord-263987-ff6kor0c	241	2	work	work	NN
cord-263987-ff6kor0c	241	3	by	by	IN
cord-263987-ff6kor0c	241	4	Rivas	Rivas	NNP
cord-263987-ff6kor0c	241	5	and	and	CC
cord-263987-ff6kor0c	241	6	Eddy	Eddy	NNP
cord-263987-ff6kor0c	241	7	[	[	-LRB-
cord-263987-ff6kor0c	241	8	56	56	CD
cord-263987-ff6kor0c	241	9	]	]	-RRB-
cord-263987-ff6kor0c	242	1	and	and	CC
cord-263987-ff6kor0c	242	2	by	by	IN
cord-263987-ff6kor0c	242	3	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	242	4	[	[	-LRB-
cord-263987-ff6kor0c	242	5	53	53	CD
cord-263987-ff6kor0c	242	6	]	]	-RRB-
cord-263987-ff6kor0c	242	7	[	[	-LRB-
cord-263987-ff6kor0c	242	8	54	54	CD
cord-263987-ff6kor0c	242	9	]	]	-RRB-
cord-263987-ff6kor0c	243	1	[	[	-LRB-
cord-263987-ff6kor0c	243	2	55	55	CD
cord-263987-ff6kor0c	243	3	]	]	-RRB-
cord-263987-ff6kor0c	243	4	may	may	MD
cord-263987-ff6kor0c	243	5	be	be	VB
cord-263987-ff6kor0c	243	6	interpreted	interpret	VBN
cord-263987-ff6kor0c	243	7	as	as	IN
cord-263987-ff6kor0c	243	8	both	both	CC
cord-263987-ff6kor0c	243	9	good	good	JJ
cord-263987-ff6kor0c	243	10	and	and	CC
cord-263987-ff6kor0c	243	11	bad	bad	JJ
cord-263987-ff6kor0c	243	12	news	news	NN
cord-263987-ff6kor0c	243	13	for	for	IN
cord-263987-ff6kor0c	243	14	automata	automata	NN
cord-263987-ff6kor0c	243	15	-	-	HYPH
cord-263987-ff6kor0c	243	16	theoretic	theoretic	JJ
cord-263987-ff6kor0c	243	17	approaches	approach	NNS
cord-263987-ff6kor0c	243	18	.	.	.
cord-263987-ff6kor0c	244	1	It	-PRON-	PRP
cord-263987-ff6kor0c	244	2	appears	appear	VBZ
cord-263987-ff6kor0c	244	3	that	that	IN
cord-263987-ff6kor0c	244	4	closed	closed	JJ
cord-263987-ff6kor0c	244	5	-	-	HYPH
cord-263987-ff6kor0c	244	6	form	form	NN
cord-263987-ff6kor0c	244	7	solutions	solution	NNS
cord-263987-ff6kor0c	244	8	for	for	IN
cord-263987-ff6kor0c	244	9	observed	observed	JJ
cord-263987-ff6kor0c	244	10	gap	gap	NN
cord-263987-ff6kor0c	244	11	length	length	NN
cord-263987-ff6kor0c	244	12	distributions	distribution	NNS
cord-263987-ff6kor0c	244	13	at	at	IN
cord-263987-ff6kor0c	244	14	finite	finite	JJ
cord-263987-ff6kor0c	244	15	times	time	NNS
cord-263987-ff6kor0c	244	16	,	,	,
cord-263987-ff6kor0c	244	17	and	and	CC
cord-263987-ff6kor0c	244	18	in	in	IN
cord-263987-ff6kor0c	244	19	particular	particular	JJ
cord-263987-ff6kor0c	244	20	the	the	DT
cord-263987-ff6kor0c	244	21	geometric	geometric	JJ
cord-263987-ff6kor0c	244	22	distributions	distribution	NNS
cord-263987-ff6kor0c	244	23	that	that	WDT
cord-263987-ff6kor0c	244	24	simple	simple	JJ
cord-263987-ff6kor0c	244	25	automata	automata	NN
cord-263987-ff6kor0c	244	26	are	be	VBP
cord-263987-ff6kor0c	244	27	good	good	JJ
cord-263987-ff6kor0c	244	28	at	at	IN
cord-263987-ff6kor0c	244	29	modeling	modeling	NN
cord-263987-ff6kor0c	244	30	,	,	,
cord-263987-ff6kor0c	244	31	are	be	VBP
cord-263987-ff6kor0c	244	32	still	still	RB
cord-263987-ff6kor0c	244	33	out	out	IN
cord-263987-ff6kor0c	244	34	of	of	IN
cord-263987-ff6kor0c	244	35	reach	reach	NN
cord-263987-ff6kor0c	244	36	for	for	IN
cord-263987-ff6kor0c	244	37	realistic	realistic	JJ
cord-263987-ff6kor0c	244	38	indel	indel	NN
cord-263987-ff6kor0c	244	39	models	model	NNS
cord-263987-ff6kor0c	244	40	,	,	,
cord-263987-ff6kor0c	244	41	and	and	CC
cord-263987-ff6kor0c	244	42	indeed	indeed	RB
cord-263987-ff6kor0c	244	43	(	(	-LRB-
cord-263987-ff6kor0c	244	44	for	for	IN
cord-263987-ff6kor0c	244	45	simple	simple	JJ
cord-263987-ff6kor0c	244	46	models	model	NNS
cord-263987-ff6kor0c	244	47	)	)	-RRB-
cord-263987-ff6kor0c	244	48	have	have	VBP
cord-263987-ff6kor0c	244	49	been	be	VBN
cord-263987-ff6kor0c	244	50	proven	prove	VBN
cord-263987-ff6kor0c	244	51	impossible	impossible	JJ
cord-263987-ff6kor0c	244	52	[	[	-LRB-
cord-263987-ff6kor0c	244	53	56	56	CD
cord-263987-ff6kor0c	244	54	]	]	-RRB-
cord-263987-ff6kor0c	244	55	.	.	.
cord-263987-ff6kor0c	245	1	Further	further	RB
cord-263987-ff6kor0c	245	2	,	,	,
cord-263987-ff6kor0c	245	3	simulation	simulation	NN
cord-263987-ff6kor0c	245	4	results	result	NNS
cord-263987-ff6kor0c	245	5	have	have	VBP
cord-263987-ff6kor0c	245	6	demonstrated	demonstrate	VBN
cord-263987-ff6kor0c	245	7	that	that	IN
cord-263987-ff6kor0c	245	8	geometric	geometric	JJ
cord-263987-ff6kor0c	245	9	distributions	distribution	NNS
cord-263987-ff6kor0c	245	10	are	be	VBP
cord-263987-ff6kor0c	245	11	not	not	RB
cord-263987-ff6kor0c	245	12	a	a	DT
cord-263987-ff6kor0c	245	13	good	good	JJ
cord-263987-ff6kor0c	245	14	fit	fit	NN
cord-263987-ff6kor0c	245	15	to	to	IN
cord-263987-ff6kor0c	245	16	the	the	DT
cord-263987-ff6kor0c	245	17	observed	observed	JJ
cord-263987-ff6kor0c	245	18	gap	gap	NN
cord-263987-ff6kor0c	245	19	length	length	NN
cord-263987-ff6kor0c	245	20	distributions	distribution	NNS
cord-263987-ff6kor0c	245	21	when	when	WRB
cord-263987-ff6kor0c	245	22	the	the	DT
cord-263987-ff6kor0c	245	23	underlying	underlying	JJ
cord-263987-ff6kor0c	245	24	indel	indel	NN
cord-263987-ff6kor0c	245	25	model	model	NN
cord-263987-ff6kor0c	245	26	has	have	VBZ
cord-263987-ff6kor0c	245	27	geometrically	geometrically	RB
cord-263987-ff6kor0c	245	28	-	-	HYPH
cord-263987-ff6kor0c	245	29	distributed	distribute	VBN
cord-263987-ff6kor0c	245	30	lengths	length	NNS
cord-263987-ff6kor0c	245	31	for	for	IN
cord-263987-ff6kor0c	245	32	its	-PRON-	PRP$
cord-263987-ff6kor0c	245	33	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	245	34	indel	indel	NN
cord-263987-ff6kor0c	245	35	events	event	NNS
cord-263987-ff6kor0c	245	36	[	[	-LRB-
cord-263987-ff6kor0c	245	37	56	56	CD
cord-263987-ff6kor0c	245	38	]	]	-RRB-
cord-263987-ff6kor0c	245	39	.	.	.
cord-263987-ff6kor0c	246	1	If	if	IN
cord-263987-ff6kor0c	246	2	the	the	DT
cord-263987-ff6kor0c	246	3	lengths	length	NNS
cord-263987-ff6kor0c	246	4	of	of	IN
cord-263987-ff6kor0c	246	5	the	the	DT
cord-263987-ff6kor0c	246	6	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	246	7	indels	indel	NNS
cord-263987-ff6kor0c	246	8	follow	follow	VBP
cord-263987-ff6kor0c	246	9	biologically	biologically	RB
cord-263987-ff6kor0c	246	10	plausible	plausible	JJ
cord-263987-ff6kor0c	246	11	power	power	NN
cord-263987-ff6kor0c	246	12	-	-	HYPH
cord-263987-ff6kor0c	246	13	law	law	NN
cord-263987-ff6kor0c	246	14	distributions	distribution	NNS
cord-263987-ff6kor0c	246	15	,	,	,
cord-263987-ff6kor0c	246	16	the	the	DT
cord-263987-ff6kor0c	246	17	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	246	18	effects	effect	NNS
cord-263987-ff6kor0c	246	19	due	due	IN
cord-263987-ff6kor0c	246	20	to	to	IN
cord-263987-ff6kor0c	246	21	overlapping	overlap	VBG
cord-263987-ff6kor0c	246	22	indels	indel	NNS
cord-263987-ff6kor0c	246	23	become	become	VBP
cord-263987-ff6kor0c	246	24	larger	large	JJR
cord-263987-ff6kor0c	246	25	as	as	IN
cord-263987-ff6kor0c	246	26	the	the	DT
cord-263987-ff6kor0c	246	27	gaps	gap	NNS
cord-263987-ff6kor0c	246	28	grow	grow	VB
cord-263987-ff6kor0c	246	29	longer	long	RBR
cord-263987-ff6kor0c	246	30	[	[	-LRB-
cord-263987-ff6kor0c	246	31	54	54	CD
cord-263987-ff6kor0c	246	32	]	]	-RRB-
cord-263987-ff6kor0c	246	33	.	.	.
cord-263987-ff6kor0c	247	1	That	that	DT
cord-263987-ff6kor0c	247	2	is	be	VBZ
cord-263987-ff6kor0c	247	3	the	the	DT
cord-263987-ff6kor0c	247	4	bad	bad	JJ
cord-263987-ff6kor0c	247	5	news	news	NN
cord-263987-ff6kor0c	247	6	(	(	-LRB-
cord-263987-ff6kor0c	247	7	at	at	IN
cord-263987-ff6kor0c	247	8	least	least	JJS
cord-263987-ff6kor0c	247	9	for	for	IN
cord-263987-ff6kor0c	247	10	automata	automata	NN
cord-263987-ff6kor0c	247	11	)	)	-RRB-
cord-263987-ff6kor0c	247	12	.	.	.
cord-263987-ff6kor0c	248	1	The	the	DT
cord-263987-ff6kor0c	248	2	good	good	JJ
cord-263987-ff6kor0c	248	3	news	news	NN
cord-263987-ff6kor0c	248	4	is	be	VBZ
cord-263987-ff6kor0c	248	5	that	that	IN
cord-263987-ff6kor0c	248	6	the	the	DT
cord-263987-ff6kor0c	248	7	simulation	simulation	NN
cord-263987-ff6kor0c	248	8	results	result	NNS
cord-263987-ff6kor0c	248	9	also	also	RB
cord-263987-ff6kor0c	248	10	suggest	suggest	VBP
cord-263987-ff6kor0c	248	11	that	that	IN
cord-263987-ff6kor0c	248	12	,	,	,
cord-263987-ff6kor0c	248	13	for	for	IN
cord-263987-ff6kor0c	248	14	short	short	JJ
cord-263987-ff6kor0c	248	15	branches	branch	NNS
cord-263987-ff6kor0c	248	16	and/or	and/or	CC
cord-263987-ff6kor0c	248	17	gaps	gap	NNS
cord-263987-ff6kor0c	248	18	(	(	-LRB-
cord-263987-ff6kor0c	248	19	such	such	JJ
cord-263987-ff6kor0c	248	20	that	that	IN
cord-263987-ff6kor0c	248	21	indels	indel	NNS
cord-263987-ff6kor0c	248	22	rarely	rarely	RB
cord-263987-ff6kor0c	248	23	overlap	overlap	VBP
cord-263987-ff6kor0c	248	24	)	)	-RRB-
cord-263987-ff6kor0c	248	25	,	,	,
cord-263987-ff6kor0c	248	26	the	the	DT
cord-263987-ff6kor0c	248	27	error	error	NN
cord-263987-ff6kor0c	248	28	may	may	MD
cord-263987-ff6kor0c	248	29	not	not	RB
cord-263987-ff6kor0c	248	30	be	be	VB
cord-263987-ff6kor0c	248	31	too	too	RB
cord-263987-ff6kor0c	248	32	bad	bad	JJ
cord-263987-ff6kor0c	248	33	to	to	TO
cord-263987-ff6kor0c	248	34	live	live	VB
cord-263987-ff6kor0c	248	35	with	with	IN
cord-263987-ff6kor0c	248	36	.	.	.
cord-263987-ff6kor0c	249	1	Approximate	approximate	JJ
cord-263987-ff6kor0c	249	2	-	-	HYPH
cord-263987-ff6kor0c	249	3	fit	fit	JJ
cord-263987-ff6kor0c	249	4	approaches	approach	NNS
cord-263987-ff6kor0c	249	5	that	that	WDT
cord-263987-ff6kor0c	249	6	are	be	VBP
cord-263987-ff6kor0c	249	7	common	common	JJ
cord-263987-ff6kor0c	249	8	in	in	IN
cord-263987-ff6kor0c	249	9	Pair	pair	NN
cord-263987-ff6kor0c	249	10	HMM	HMM	NNP
cord-263987-ff6kor0c	249	11	modeling	model	VBG
cord-263987-ff6kor0c	249	12	and	and	CC
cord-263987-ff6kor0c	249	13	pairwise	pairwise	JJ
cord-263987-ff6kor0c	249	14	sequence	sequence	NN
cord-263987-ff6kor0c	249	15	alignment	alignment	NN
cord-263987-ff6kor0c	249	16	-	-	:
cord-263987-ff6kor0c	249	17	such	such	JJ
cord-263987-ff6kor0c	249	18	as	as	IN
cord-263987-ff6kor0c	249	19	using	use	VBG
cord-263987-ff6kor0c	249	20	a	a	DT
cord-263987-ff6kor0c	249	21	mixture	mixture	NN
cord-263987-ff6kor0c	249	22	of	of	IN
cord-263987-ff6kor0c	249	23	geometric	geometric	JJ
cord-263987-ff6kor0c	249	24	distributions	distribution	NNS
cord-263987-ff6kor0c	249	25	to	to	TO
cord-263987-ff6kor0c	249	26	approximate	approximate	VB
cord-263987-ff6kor0c	249	27	a	a	DT
cord-263987-ff6kor0c	249	28	gap	gap	NN
cord-263987-ff6kor0c	249	29	length	length	NN
cord-263987-ff6kor0c	249	30	distribution	distribution	NN
cord-263987-ff6kor0c	249	31	(	(	-LRB-
cord-263987-ff6kor0c	249	32	yielding	yield	VBG
cord-263987-ff6kor0c	249	33	a	a	DT
cord-263987-ff6kor0c	249	34	longer	long	JJR
cord-263987-ff6kor0c	249	35	tail	tail	NN
cord-263987-ff6kor0c	249	36	than	than	IN
cord-263987-ff6kor0c	249	37	can	can	MD
cord-263987-ff6kor0c	249	38	be	be	VB
cord-263987-ff6kor0c	249	39	modeled	model	VBN
cord-263987-ff6kor0c	249	40	using	use	VBG
cord-263987-ff6kor0c	249	41	a	a	DT
cord-263987-ff6kor0c	249	42	pure	pure	JJ
cord-263987-ff6kor0c	249	43	geometric	geometric	JJ
cord-263987-ff6kor0c	249	44	distribution)may	distribution)may	TO
cord-263987-ff6kor0c	249	45	help	help	NN
cord-263987-ff6kor0c	249	46	bridge	bridge	VB
cord-263987-ff6kor0c	249	47	the	the	DT
cord-263987-ff6kor0c	249	48	accuracy	accuracy	NN
cord-263987-ff6kor0c	249	49	gap	gap	NN
cord-263987-ff6kor0c	249	50	[	[	-LRB-
cord-263987-ff6kor0c	249	51	96	96	CD
cord-263987-ff6kor0c	249	52	]	]	-RRB-
cord-263987-ff6kor0c	249	53	.	.	.
cord-263987-ff6kor0c	250	1	Given	give	VBN
cord-263987-ff6kor0c	250	2	the	the	DT
cord-263987-ff6kor0c	250	3	power	power	NN
cord-263987-ff6kor0c	250	4	of	of	IN
cord-263987-ff6kor0c	250	5	automata	automata	NN
cord-263987-ff6kor0c	250	6	-	-	HYPH
cord-263987-ff6kor0c	250	7	theoretic	theoretic	JJ
cord-263987-ff6kor0c	250	8	approaches	approach	NNS
cord-263987-ff6kor0c	250	9	,	,	,
cord-263987-ff6kor0c	250	10	the	the	DT
cord-263987-ff6kor0c	250	11	best	good	JJS
cord-263987-ff6kor0c	250	12	way	way	NN
cord-263987-ff6kor0c	250	13	forward	forward	RB
cord-263987-ff6kor0c	250	14	(	(	-LRB-
cord-263987-ff6kor0c	250	15	in	in	IN
cord-263987-ff6kor0c	250	16	the	the	DT
cord-263987-ff6kor0c	250	17	absence	absence	NN
cord-263987-ff6kor0c	250	18	of	of	IN
cord-263987-ff6kor0c	250	19	a	a	DT
cord-263987-ff6kor0c	250	20	closed	closed	JJ
cord-263987-ff6kor0c	250	21	-	-	HYPH
cord-263987-ff6kor0c	250	22	form	form	NN
cord-263987-ff6kor0c	250	23	solution	solution	NN
cord-263987-ff6kor0c	250	24	)	)	-RRB-
cord-263987-ff6kor0c	250	25	may	may	MD
cord-263987-ff6kor0c	250	26	be	be	VB
cord-263987-ff6kor0c	250	27	to	to	TO
cord-263987-ff6kor0c	250	28	embrace	embrace	VB
cord-263987-ff6kor0c	250	29	such	such	JJ
cord-263987-ff6kor0c	250	30	approximations	approximation	NNS
cord-263987-ff6kor0c	250	31	and	and	CC
cord-263987-ff6kor0c	250	32	live	live	VBP
cord-263987-ff6kor0c	250	33	with	with	IN
cord-263987-ff6kor0c	250	34	the	the	DT
cord-263987-ff6kor0c	250	35	ensuing	ensue	VBG
cord-263987-ff6kor0c	250	36	error	error	NN
cord-263987-ff6kor0c	250	37	.	.	.
cord-263987-ff6kor0c	251	1	Interestingly	interestingly	RB
cord-263987-ff6kor0c	251	2	,	,	,
cord-263987-ff6kor0c	251	3	the	the	DT
cord-263987-ff6kor0c	251	4	authors	author	NNS
cord-263987-ff6kor0c	251	5	of	of	IN
cord-263987-ff6kor0c	251	6	the	the	DT
cord-263987-ff6kor0c	251	7	two	two	CD
cord-263987-ff6kor0c	251	8	recent	recent	JJ
cord-263987-ff6kor0c	251	9	simulation	simulation	NN
cord-263987-ff6kor0c	251	10	studies	study	NNS
cord-263987-ff6kor0c	251	11	that	that	WDT
cord-263987-ff6kor0c	251	12	prompted	prompt	VBD
cord-263987-ff6kor0c	251	13	this	this	DT
cord-263987-ff6kor0c	251	14	commentary	commentary	NN
cord-263987-ff6kor0c	251	15	come	come	VB
cord-263987-ff6kor0c	251	16	to	to	IN
cord-263987-ff6kor0c	251	17	different	different	JJ
cord-263987-ff6kor0c	251	18	conclusions	conclusion	NNS
cord-263987-ff6kor0c	251	19	about	about	IN
cord-263987-ff6kor0c	251	20	the	the	DT
cord-263987-ff6kor0c	251	21	viability	viability	NN
cord-263987-ff6kor0c	251	22	of	of	IN
cord-263987-ff6kor0c	251	23	automatabased	automatabased	JJ
cord-263987-ff6kor0c	251	24	dynamic	dynamic	JJ
cord-263987-ff6kor0c	251	25	programming	programming	NN
cord-263987-ff6kor0c	251	26	approaches	approach	NNS
cord-263987-ff6kor0c	251	27	.	.	.
cord-263987-ff6kor0c	252	1	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	252	2	[	[	-LRB-
cord-263987-ff6kor0c	252	3	53	53	CD
cord-263987-ff6kor0c	252	4	,	,	,
cord-263987-ff6kor0c	252	5	54	54	CD
cord-263987-ff6kor0c	252	6	]	]	-RRB-
cord-263987-ff6kor0c	252	7	,	,	,
cord-263987-ff6kor0c	252	8	arguing	argue	VBG
cord-263987-ff6kor0c	252	9	that	that	IN
cord-263987-ff6kor0c	252	10	realism	realism	NN
cord-263987-ff6kor0c	252	11	is	be	VBZ
cord-263987-ff6kor0c	252	12	paramount	paramount	NN
cord-263987-ff6kor0c	252	13	,	,	,
cord-263987-ff6kor0c	252	14	advocates	advocate	VBZ
cord-263987-ff6kor0c	252	15	deeper	deep	JJR
cord-263987-ff6kor0c	252	16	study	study	NN
cord-263987-ff6kor0c	252	17	of	of	IN
cord-263987-ff6kor0c	252	18	the	the	DT
cord-263987-ff6kor0c	252	19	gap	gap	NN
cord-263987-ff6kor0c	252	20	length	length	NN
cord-263987-ff6kor0c	252	21	distributions	distribution	NNS
cord-263987-ff6kor0c	252	22	obtained	obtain	VBN
cord-263987-ff6kor0c	252	23	from	from	IN
cord-263987-ff6kor0c	252	24	simple	simple	JJ
cord-263987-ff6kor0c	252	25	instantaneous	instantaneous	JJ
cord-263987-ff6kor0c	252	26	models	model	NNS
cord-263987-ff6kor0c	252	27	-	-	:
cord-263987-ff6kor0c	252	28	while	while	IN
cord-263987-ff6kor0c	252	29	acknowledging	acknowledge	VBG
cord-263987-ff6kor0c	252	30	that	that	IN
cord-263987-ff6kor0c	252	31	such	such	JJ
cord-263987-ff6kor0c	252	32	gap	gap	NN
cord-263987-ff6kor0c	252	33	length	length	NN
cord-263987-ff6kor0c	252	34	distributions	distribution	NNS
cord-263987-ff6kor0c	252	35	may	may	MD
cord-263987-ff6kor0c	252	36	be	be	VB
cord-263987-ff6kor0c	252	37	more	more	RBR
cord-263987-ff6kor0c	252	38	difficult	difficult	JJ
cord-263987-ff6kor0c	252	39	to	to	TO
cord-263987-ff6kor0c	252	40	use	use	VB
cord-263987-ff6kor0c	252	41	in	in	IN
cord-263987-ff6kor0c	252	42	practice	practice	NN
cord-263987-ff6kor0c	252	43	than	than	IN
cord-263987-ff6kor0c	252	44	the	the	DT
cord-263987-ff6kor0c	252	45	simple	simple	JJ
cord-263987-ff6kor0c	252	46	geometric	geometric	JJ
cord-263987-ff6kor0c	252	47	distributions	distribution	NNS
cord-263987-ff6kor0c	252	48	offered	offer	VBN
cord-263987-ff6kor0c	252	49	by	by	IN
cord-263987-ff6kor0c	252	50	HMM	HMM	NNP
cord-263987-ff6kor0c	252	51	-	-	HYPH
cord-263987-ff6kor0c	252	52	like	like	JJ
cord-263987-ff6kor0c	252	53	models	model	NNS
cord-263987-ff6kor0c	252	54	.	.	.
cord-263987-ff6kor0c	253	1	Rivas	Rivas	NNP
cord-263987-ff6kor0c	253	2	and	and	CC
cord-263987-ff6kor0c	253	3	Eddy	Eddy	NNP
cord-263987-ff6kor0c	253	4	[	[	-LRB-
cord-263987-ff6kor0c	253	5	56	56	CD
cord-263987-ff6kor0c	253	6	]	]	-RRB-
cord-263987-ff6kor0c	253	7	,	,	,
cord-263987-ff6kor0c	253	8	clearly	clearly	RB
cord-263987-ff6kor0c	253	9	targeting	target	VBG
cord-263987-ff6kor0c	253	10	applications	application	NNS
cord-263987-ff6kor0c	253	11	(	(	-LRB-
cord-263987-ff6kor0c	253	12	particularly	particularly	RB
cord-263987-ff6kor0c	253	13	those	those	DT
cord-263987-ff6kor0c	253	14	such	such	JJ
cord-263987-ff6kor0c	253	15	as	as	IN
cord-263987-ff6kor0c	253	16	profile	profile	NN
cord-263987-ff6kor0c	253	17	HMMs	HMMs	NNP
cord-263987-ff6kor0c	253	18	)	)	-RRB-
cord-263987-ff6kor0c	253	19	,	,	,
cord-263987-ff6kor0c	253	20	work	work	VBP
cord-263987-ff6kor0c	253	21	backward	backward	RB
cord-263987-ff6kor0c	253	22	from	from	IN
cord-263987-ff6kor0c	253	23	HMMlike	hmmlike	JJ
cord-263987-ff6kor0c	253	24	models	model	NNS
cord-263987-ff6kor0c	253	25	toward	toward	IN
cord-263987-ff6kor0c	253	26	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	253	27	models	model	NNS
cord-263987-ff6kor0c	253	28	with	with	IN
cord-263987-ff6kor0c	253	29	embedded	embed	VBN
cord-263987-ff6kor0c	253	30	hidden	hide	VBN
cord-263987-ff6kor0c	253	31	information	information	NN
cord-263987-ff6kor0c	253	32	.	.	.
cord-263987-ff6kor0c	254	1	These	these	DT
cord-263987-ff6kor0c	254	2	models	model	NNS
cord-263987-ff6kor0c	254	3	may	may	MD
cord-263987-ff6kor0c	254	4	be	be	VB
cord-263987-ff6kor0c	254	5	somewhat	somewhat	RB
cord-263987-ff6kor0c	254	6	mathematically	mathematically	RB
cord-263987-ff6kor0c	254	7	contrived	contrived	JJ
cord-263987-ff6kor0c	254	8	,	,	,
cord-263987-ff6kor0c	254	9	but	but	CC
cord-263987-ff6kor0c	254	10	are	be	VBP
cord-263987-ff6kor0c	254	11	easier	easy	JJR
cord-263987-ff6kor0c	254	12	to	to	TO
cord-263987-ff6kor0c	254	13	tailor	tailor	VB
cord-263987-ff6kor0c	254	14	so	so	IN
cord-263987-ff6kor0c	254	15	as	as	IN
cord-263987-ff6kor0c	254	16	to	to	TO
cord-263987-ff6kor0c	254	17	model	model	VB
cord-263987-ff6kor0c	254	18	effects	effect	NNS
cord-263987-ff6kor0c	254	19	such	such	JJ
cord-263987-ff6kor0c	254	20	as	as	IN
cord-263987-ff6kor0c	254	21	position	position	NN
cord-263987-ff6kor0c	254	22	-	-	HYPH
cord-263987-ff6kor0c	254	23	specific	specific	JJ
cord-263987-ff6kor0c	254	24	conservation	conservation	NN
cord-263987-ff6kor0c	254	25	,	,	,
cord-263987-ff6kor0c	254	26	thus	thus	RB
cord-263987-ff6kor0c	254	27	trading	trade	VBG
cord-263987-ff6kor0c	254	28	(	(	-LRB-
cord-263987-ff6kor0c	254	29	in	in	IN
cord-263987-ff6kor0c	254	30	a	a	DT
cord-263987-ff6kor0c	254	31	certain	certain	JJ
cord-263987-ff6kor0c	254	32	sense	sense	NN
cord-263987-ff6kor0c	254	33	)	)	-RRB-
cord-263987-ff6kor0c	254	34	purism	purism	NN
cord-263987-ff6kor0c	254	35	for	for	IN
cord-263987-ff6kor0c	254	36	expressiveness	expressiveness	NN
cord-263987-ff6kor0c	254	37	.	.	.
cord-263987-ff6kor0c	255	1	Whichever	whichever	WDT
cord-263987-ff6kor0c	255	2	approach	approach	NN
cord-263987-ff6kor0c	255	3	is	be	VBZ
cord-263987-ff6kor0c	255	4	used	use	VBN
cord-263987-ff6kor0c	255	5	,	,	,
cord-263987-ff6kor0c	255	6	these	these	DT
cord-263987-ff6kor0c	255	7	results	result	NNS
cord-263987-ff6kor0c	255	8	are	be	VBP
cord-263987-ff6kor0c	255	9	unambiguously	unambiguously	RB
cord-263987-ff6kor0c	255	10	good	good	JJ
cord-263987-ff6kor0c	255	11	news	news	NN
cord-263987-ff6kor0c	255	12	for	for	IN
cord-263987-ff6kor0c	255	13	the	the	DT
cord-263987-ff6kor0c	255	14	theoretical	theoretical	JJ
cord-263987-ff6kor0c	255	15	study	study	NN
cord-263987-ff6kor0c	255	16	of	of	IN
cord-263987-ff6kor0c	255	17	indel	indel	NN
cord-263987-ff6kor0c	255	18	processes	process	NNS
cord-263987-ff6kor0c	255	19	.	.	.
cord-263987-ff6kor0c	256	1	The	the	DT
cord-263987-ff6kor0c	256	2	potential	potential	JJ
cord-263987-ff6kor0c	256	3	benefits	benefit	NNS
cord-263987-ff6kor0c	256	4	of	of	IN
cord-263987-ff6kor0c	256	5	modeling	model	VBG
cord-263987-ff6kor0c	256	6	alignment	alignment	NN
cord-263987-ff6kor0c	256	7	as	as	IN
cord-263987-ff6kor0c	256	8	an	an	DT
cord-263987-ff6kor0c	256	9	aspect	aspect	NN
cord-263987-ff6kor0c	256	10	of	of	IN
cord-263987-ff6kor0c	256	11	statistical	statistical	JJ
cord-263987-ff6kor0c	256	12	phylogenetics	phylogenetic	NNS
cord-263987-ff6kor0c	256	13	are	be	VBP
cord-263987-ff6kor0c	256	14	significant	significant	JJ
cord-263987-ff6kor0c	256	15	.	.	.
cord-263987-ff6kor0c	257	1	One	one	PRP
cord-263987-ff6kor0c	257	2	can	can	MD
cord-263987-ff6kor0c	257	3	reasonably	reasonably	RB
cord-263987-ff6kor0c	257	4	hope	hope	VB
cord-263987-ff6kor0c	257	5	that	that	IN
cord-263987-ff6kor0c	257	6	the	the	DT
cord-263987-ff6kor0c	257	7	advance	advance	NN
cord-263987-ff6kor0c	257	8	of	of	IN
cord-263987-ff6kor0c	257	9	theoretical	theoretical	JJ
cord-263987-ff6kor0c	257	10	work	work	NN
cord-263987-ff6kor0c	257	11	in	in	IN
cord-263987-ff6kor0c	257	12	this	this	DT
cord-263987-ff6kor0c	257	13	area	area	NN
cord-263987-ff6kor0c	257	14	will	will	MD
cord-263987-ff6kor0c	257	15	continue	continue	VB
cord-263987-ff6kor0c	257	16	to	to	TO
cord-263987-ff6kor0c	257	17	inform	inform	VB
cord-263987-ff6kor0c	257	18	advances	advance	NNS
cord-263987-ff6kor0c	257	19	in	in	IN
cord-263987-ff6kor0c	257	20	both	both	DT
cord-263987-ff6kor0c	257	21	bioinformatics	bioinformatic	NNS
cord-263987-ff6kor0c	257	22	and	and	CC
cord-263987-ff6kor0c	257	23	statistical	statistical	JJ
cord-263987-ff6kor0c	257	24	phylogenetics	phylogenetic	NNS
cord-263987-ff6kor0c	257	25	.	.	.
cord-263987-ff6kor0c	258	1	After	after	RB
cord-263987-ff6kor0c	258	2	all	all	RB
cord-263987-ff6kor0c	258	3	,	,	,
cord-263987-ff6kor0c	258	4	and	and	CC
cord-263987-ff6kor0c	258	5	in	in	IN
cord-263987-ff6kor0c	258	6	spite	spite	NN
cord-263987-ff6kor0c	258	7	of	of	IN
cord-263987-ff6kor0c	258	8	the	the	DT
cord-263987-ff6kor0c	258	9	Cambrian	Cambrian	NNP
cord-263987-ff6kor0c	258	10	explosion	explosion	NN
cord-263987-ff6kor0c	258	11	in	in	IN
cord-263987-ff6kor0c	258	12	bioinformatics	bioinformatics	NN
cord-263987-ff6kor0c	258	13	subdisciplines	subdiscipline	NNS
cord-263987-ff6kor0c	258	14	,	,	,
cord-263987-ff6kor0c	258	15	sequence	sequence	NN
cord-263987-ff6kor0c	258	16	alignment	alignment	NN
cord-263987-ff6kor0c	258	17	and	and	CC
cord-263987-ff6kor0c	258	18	phylogeny	phylogeny	NN
cord-263987-ff6kor0c	258	19	truly	truly	RB
cord-263987-ff6kor0c	258	20	are	be	VBP
cord-263987-ff6kor0c	258	21	closely	closely	RB
cord-263987-ff6kor0c	258	22	related	relate	VBN
cord-263987-ff6kor0c	258	23	aspects	aspect	NNS
cord-263987-ff6kor0c	258	24	of	of	IN
cord-263987-ff6kor0c	258	25	mathematical	mathematical	JJ
cord-263987-ff6kor0c	258	26	biology	biology	NN
cord-263987-ff6kor0c	258	27	.	.	.
cord-263987-ff6kor0c	259	1	Evolution	evolution	NN
cord-263987-ff6kor0c	259	2	of	of	IN
cord-263987-ff6kor0c	259	3	protein	protein	NN
cord-263987-ff6kor0c	260	1	molecules	molecule	NNS
cord-263987-ff6kor0c	260	2	A	a	DT
cord-263987-ff6kor0c	260	3	model	model	NN
cord-263987-ff6kor0c	260	4	of	of	IN
cord-263987-ff6kor0c	260	5	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	260	6	change	change	NN
cord-263987-ff6kor0c	260	7	in	in	IN
cord-263987-ff6kor0c	260	8	proteins	protein	NNS
cord-263987-ff6kor0c	260	9	Atlas	Atlas	NNP
cord-263987-ff6kor0c	260	10	of	of	IN
cord-263987-ff6kor0c	260	11	Protein	Protein	NNP
cord-263987-ff6kor0c	260	12	Sequence	Sequence	NNP
cord-263987-ff6kor0c	260	13	and	and	CC
cord-263987-ff6kor0c	260	14	Structure	structure	NN
cord-263987-ff6kor0c	261	1	In	in	IN
cord-263987-ff6kor0c	261	2	Evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	261	3	trees	tree	NNS
cord-263987-ff6kor0c	261	4	from	from	IN
cord-263987-ff6kor0c	261	5	DNA	dna	NN
cord-263987-ff6kor0c	261	6	sequences	sequence	NNS
cord-263987-ff6kor0c	261	7	:	:	:
cord-263987-ff6kor0c	261	8	a	a	DT
cord-263987-ff6kor0c	261	9	maximum	maximum	JJ
cord-263987-ff6kor0c	261	10	likelihood	likelihood	NN
cord-263987-ff6kor0c	261	11	approach	approach	NN
cord-263987-ff6kor0c	261	12	Maximum	maximum	NN
cord-263987-ff6kor0c	261	13	-	-	HYPH
cord-263987-ff6kor0c	261	14	likelihood	likelihood	NN
cord-263987-ff6kor0c	261	15	estimation	estimation	NN
cord-263987-ff6kor0c	261	16	of	of	IN
cord-263987-ff6kor0c	261	17	phylogeny	phylogeny	NN
cord-263987-ff6kor0c	261	18	from	from	IN
cord-263987-ff6kor0c	261	19	DNA	dna	NN
cord-263987-ff6kor0c	261	20	sequences	sequence	NNS
cord-263987-ff6kor0c	261	21	when	when	WRB
cord-263987-ff6kor0c	261	22	substitution	substitution	NN
cord-263987-ff6kor0c	261	23	rates	rate	NNS
cord-263987-ff6kor0c	261	24	differ	differ	VBP
cord-263987-ff6kor0c	261	25	over	over	IN
cord-263987-ff6kor0c	261	26	sites	site	NNS
cord-263987-ff6kor0c	261	27	Maximum	maximum	JJ
cord-263987-ff6kor0c	261	28	likelihood	likelihood	NN
cord-263987-ff6kor0c	261	29	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	261	30	estimation	estimation	NN
cord-263987-ff6kor0c	261	31	from	from	IN
cord-263987-ff6kor0c	261	32	DNA	dna	NN
cord-263987-ff6kor0c	261	33	sequences	sequence	NNS
cord-263987-ff6kor0c	261	34	with	with	IN
cord-263987-ff6kor0c	261	35	variable	variable	JJ
cord-263987-ff6kor0c	261	36	rates	rate	NNS
cord-263987-ff6kor0c	261	37	over	over	IN
cord-263987-ff6kor0c	261	38	sites	site	NNS
cord-263987-ff6kor0c	261	39	:	:	:
cord-263987-ff6kor0c	261	40	approximate	approximate	JJ
cord-263987-ff6kor0c	261	41	methods	method	NNS
cord-263987-ff6kor0c	261	42	Gene	Gene	NNP
cord-263987-ff6kor0c	261	43	finding	find	VBG
cord-263987-ff6kor0c	261	44	with	with	IN
cord-263987-ff6kor0c	261	45	a	a	DT
cord-263987-ff6kor0c	261	46	hidden	hide	VBN
cord-263987-ff6kor0c	261	47	Markov	Markov	NNP
cord-263987-ff6kor0c	261	48	model	model	NN
cord-263987-ff6kor0c	261	49	of	of	IN
cord-263987-ff6kor0c	261	50	genome	genome	NN
cord-263987-ff6kor0c	261	51	structure	structure	NN
cord-263987-ff6kor0c	261	52	and	and	CC
cord-263987-ff6kor0c	261	53	evolution	evolution	NN
cord-263987-ff6kor0c	261	54	Combining	combine	VBG
cord-263987-ff6kor0c	261	55	phylogenetic	phylogenetic	NN
cord-263987-ff6kor0c	261	56	and	and	CC
cord-263987-ff6kor0c	261	57	hidden	hide	VBN
cord-263987-ff6kor0c	261	58	Markov	Markov	NNP
cord-263987-ff6kor0c	261	59	models	model	NNS
cord-263987-ff6kor0c	261	60	in	in	IN
cord-263987-ff6kor0c	261	61	biosequence	biosequence	NNP
cord-263987-ff6kor0c	261	62	analysis	analysis	NN
cord-263987-ff6kor0c	261	63	Identification	identification	NN
cord-263987-ff6kor0c	261	64	and	and	CC
cord-263987-ff6kor0c	261	65	classification	classification	NN
cord-263987-ff6kor0c	261	66	of	of	IN
cord-263987-ff6kor0c	261	67	conserved	conserve	VBN
cord-263987-ff6kor0c	261	68	RNA	RNA	NNP
cord-263987-ff6kor0c	261	69	secondary	secondary	JJ
cord-263987-ff6kor0c	261	70	structures	structure	NNS
cord-263987-ff6kor0c	261	71	in	in	IN
cord-263987-ff6kor0c	261	72	the	the	DT
cord-263987-ff6kor0c	261	73	human	human	JJ
cord-263987-ff6kor0c	261	74	genome	genome	NN
cord-263987-ff6kor0c	262	1	An	an	DT
cord-263987-ff6kor0c	262	2	RNA	RNA	NNP
cord-263987-ff6kor0c	262	3	gene	gene	NN
cord-263987-ff6kor0c	262	4	expressed	express	VBN
cord-263987-ff6kor0c	262	5	during	during	IN
cord-263987-ff6kor0c	262	6	cortical	cortical	JJ
cord-263987-ff6kor0c	262	7	development	development	NN
cord-263987-ff6kor0c	262	8	evolved	evolve	VBD
cord-263987-ff6kor0c	262	9	rapidly	rapidly	RB
cord-263987-ff6kor0c	262	10	in	in	IN
cord-263987-ff6kor0c	262	11	humans	human	NNS
cord-263987-ff6kor0c	263	1	A	a	DT
cord-263987-ff6kor0c	263	2	comparative	comparative	JJ
cord-263987-ff6kor0c	263	3	method	method	NN
cord-263987-ff6kor0c	263	4	for	for	IN
cord-263987-ff6kor0c	263	5	finding	find	VBG
cord-263987-ff6kor0c	263	6	and	and	CC
cord-263987-ff6kor0c	263	7	folding	fold	VBG
cord-263987-ff6kor0c	263	8	RNA	RNA	NNP
cord-263987-ff6kor0c	263	9	secondary	secondary	JJ
cord-263987-ff6kor0c	263	10	structures	structure	NNS
cord-263987-ff6kor0c	263	11	within	within	IN
cord-263987-ff6kor0c	263	12	protein	protein	NN
cord-263987-ff6kor0c	263	13	-	-	HYPH
cord-263987-ff6kor0c	263	14	coding	code	VBG
cord-263987-ff6kor0c	263	15	regions	region	NNS
cord-263987-ff6kor0c	264	1	Evolutionarily	evolutionarily	RB
cord-263987-ff6kor0c	264	2	conserved	conserve	VBN
cord-263987-ff6kor0c	264	3	elements	element	NNS
cord-263987-ff6kor0c	264	4	in	in	IN
cord-263987-ff6kor0c	264	5	vertebrate	vertebrate	NN
cord-263987-ff6kor0c	264	6	,	,	,
cord-263987-ff6kor0c	264	7	insect	insect	NN
cord-263987-ff6kor0c	264	8	,	,	,
cord-263987-ff6kor0c	264	9	worm	worm	NN
cord-263987-ff6kor0c	264	10	,	,	,
cord-263987-ff6kor0c	264	11	and	and	CC
cord-263987-ff6kor0c	264	12	yeast	yeast	NN
cord-263987-ff6kor0c	264	13	genomes	genome	NNS
cord-263987-ff6kor0c	264	14	Using	use	VBG
cord-263987-ff6kor0c	264	15	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	264	16	trees	tree	NNS
cord-263987-ff6kor0c	264	17	in	in	IN
cord-263987-ff6kor0c	264	18	protein	protein	NN
cord-263987-ff6kor0c	264	19	secondary	secondary	JJ
cord-263987-ff6kor0c	264	20	structure	structure	NN
cord-263987-ff6kor0c	264	21	prediction	prediction	NN
cord-263987-ff6kor0c	264	22	and	and	CC
cord-263987-ff6kor0c	264	23	other	other	JJ
cord-263987-ff6kor0c	264	24	comparative	comparative	JJ
cord-263987-ff6kor0c	264	25	sequence	sequence	NN
cord-263987-ff6kor0c	264	26	analyses	analysis	NNS
cord-263987-ff6kor0c	264	27	Using	use	VBG
cord-263987-ff6kor0c	264	28	protein	protein	NN
cord-263987-ff6kor0c	264	29	structural	structural	JJ
cord-263987-ff6kor0c	264	30	information	information	NN
cord-263987-ff6kor0c	264	31	in	in	IN
cord-263987-ff6kor0c	264	32	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	264	33	inference	inference	NN
cord-263987-ff6kor0c	264	34	:	:	:
cord-263987-ff6kor0c	265	1	transmembrane	transmembrane	NN
cord-263987-ff6kor0c	265	2	proteins	protein	NNS
cord-263987-ff6kor0c	265	3	Reconstructing	reconstruct	VBG
cord-263987-ff6kor0c	265	4	large	large	JJ
cord-263987-ff6kor0c	265	5	regions	region	NNS
cord-263987-ff6kor0c	265	6	of	of	IN
cord-263987-ff6kor0c	265	7	an	an	DT
cord-263987-ff6kor0c	265	8	ancestral	ancestral	JJ
cord-263987-ff6kor0c	265	9	mammalian	mammalian	JJ
cord-263987-ff6kor0c	265	10	genome	genome	NN
cord-263987-ff6kor0c	265	11	in	in	IN
cord-263987-ff6kor0c	265	12	silico	silico	NN
cord-263987-ff6kor0c	265	13	Evolution	evolution	NN
cord-263987-ff6kor0c	265	14	of	of	IN
cord-263987-ff6kor0c	265	15	coral	coral	JJ
cord-263987-ff6kor0c	265	16	pigments	pigment	NNS
cord-263987-ff6kor0c	265	17	recreated	recreate	VBD
cord-263987-ff6kor0c	265	18	Ancestral	ancestral	JJ
cord-263987-ff6kor0c	265	19	sequence	sequence	NN
cord-263987-ff6kor0c	265	20	reconstruction	reconstruction	NN
cord-263987-ff6kor0c	265	21	Crystal	Crystal	NNP
cord-263987-ff6kor0c	265	22	structure	structure	NN
cord-263987-ff6kor0c	265	23	of	of	IN
cord-263987-ff6kor0c	265	24	an	an	DT
cord-263987-ff6kor0c	265	25	ancient	ancient	JJ
cord-263987-ff6kor0c	265	26	protein	protein	NN
cord-263987-ff6kor0c	265	27	:	:	:
cord-263987-ff6kor0c	265	28	evolution	evolution	NN
cord-263987-ff6kor0c	265	29	by	by	IN
cord-263987-ff6kor0c	265	30	conformational	conformational	JJ
cord-263987-ff6kor0c	265	31	epistasis	epistasis	NN
cord-263987-ff6kor0c	265	32	Palaeotemperature	Palaeotemperature	NNP
cord-263987-ff6kor0c	265	33	trend	trend	NN
cord-263987-ff6kor0c	265	34	for	for	IN
cord-263987-ff6kor0c	265	35	Precambrian	precambrian	JJ
cord-263987-ff6kor0c	265	36	life	life	NN
cord-263987-ff6kor0c	265	37	inferred	infer	VBN
cord-263987-ff6kor0c	265	38	from	from	IN
cord-263987-ff6kor0c	265	39	resurrected	resurrect	VBN
cord-263987-ff6kor0c	265	40	proteins	protein	NNS
cord-263987-ff6kor0c	265	41	Fast	Fast	NNP
cord-263987-ff6kor0c	265	42	M	M	NNP
cord-263987-ff6kor0c	265	43	L	l	NN
cord-263987-ff6kor0c	265	44	:	:	:
cord-263987-ff6kor0c	266	1	a	a	DT
cord-263987-ff6kor0c	266	2	web	web	NN
cord-263987-ff6kor0c	266	3	server	server	NN
cord-263987-ff6kor0c	266	4	for	for	IN
cord-263987-ff6kor0c	266	5	probabilistic	probabilistic	JJ
cord-263987-ff6kor0c	266	6	reconstruction	reconstruction	NN
cord-263987-ff6kor0c	266	7	of	of	IN
cord-263987-ff6kor0c	266	8	ancestral	ancestral	JJ
cord-263987-ff6kor0c	266	9	sequences	sequence	NNS
cord-263987-ff6kor0c	266	10	Directed	direct	VBN
cord-263987-ff6kor0c	266	11	evolution	evolution	NN
cord-263987-ff6kor0c	266	12	of	of	IN
cord-263987-ff6kor0c	266	13	sulfotransferases	sulfotransferase	NNS
cord-263987-ff6kor0c	266	14	and	and	CC
cord-263987-ff6kor0c	266	15	paraoxonases	paraoxonase	NNS
cord-263987-ff6kor0c	266	16	by	by	IN
cord-263987-ff6kor0c	266	17	ancestral	ancestral	JJ
cord-263987-ff6kor0c	266	18	libraries	library	NNS
cord-263987-ff6kor0c	267	1	AAV	AAV	NNP
cord-263987-ff6kor0c	267	2	ancestral	ancestral	JJ
cord-263987-ff6kor0c	267	3	reconstruction	reconstruction	NN
cord-263987-ff6kor0c	267	4	library	library	NN
cord-263987-ff6kor0c	267	5	enables	enable	VBZ
cord-263987-ff6kor0c	267	6	selection	selection	NN
cord-263987-ff6kor0c	267	7	of	of	IN
cord-263987-ff6kor0c	267	8	broadly	broadly	RB
cord-263987-ff6kor0c	267	9	infectious	infectious	JJ
cord-263987-ff6kor0c	267	10	viral	viral	JJ
cord-263987-ff6kor0c	267	11	variants	variant	NNS
cord-263987-ff6kor0c	267	12	Enhancing	enhance	VBG
cord-263987-ff6kor0c	267	13	the	the	DT
cord-263987-ff6kor0c	267	14	pharmaceutical	pharmaceutical	JJ
cord-263987-ff6kor0c	267	15	properties	property	NNS
cord-263987-ff6kor0c	267	16	of	of	IN
cord-263987-ff6kor0c	267	17	protein	protein	NN
cord-263987-ff6kor0c	267	18	drugs	drug	NNS
cord-263987-ff6kor0c	267	19	by	by	IN
cord-263987-ff6kor0c	267	20	ancestral	ancestral	JJ
cord-263987-ff6kor0c	267	21	sequence	sequence	NN
cord-263987-ff6kor0c	267	22	reconstruction	reconstruction	NN
cord-263987-ff6kor0c	267	23	Synthesis	synthesis	NN
cord-263987-ff6kor0c	267	24	of	of	IN
cord-263987-ff6kor0c	267	25	phylogeny	phylogeny	NN
cord-263987-ff6kor0c	267	26	and	and	CC
cord-263987-ff6kor0c	267	27	taxonomy	taxonomy	NN
cord-263987-ff6kor0c	267	28	into	into	IN
cord-263987-ff6kor0c	267	29	a	a	DT
cord-263987-ff6kor0c	267	30	comprehensive	comprehensive	JJ
cord-263987-ff6kor0c	267	31	tree	tree	NN
cord-263987-ff6kor0c	267	32	of	of	IN
cord-263987-ff6kor0c	267	33	life	life	NN
cord-263987-ff6kor0c	268	1	Protein	protein	NN
cord-263987-ff6kor0c	268	2	molecular	molecular	JJ
cord-263987-ff6kor0c	268	3	function	function	NN
cord-263987-ff6kor0c	268	4	prediction	prediction	NN
cord-263987-ff6kor0c	268	5	by	by	IN
cord-263987-ff6kor0c	268	6	Bayesian	Bayesian	NNP
cord-263987-ff6kor0c	268	7	phylogenomics	phylogenomic	NNS
cord-263987-ff6kor0c	268	8	Phylogenetic	Phylogenetic	NNP
cord-263987-ff6kor0c	268	9	diversity	diversity	NN
cord-263987-ff6kor0c	268	10	meets	meet	VBZ
cord-263987-ff6kor0c	268	11	conservation	conservation	NN
cord-263987-ff6kor0c	268	12	policy	policy	NN
cord-263987-ff6kor0c	268	13	:	:	:
cord-263987-ff6kor0c	268	14	small	small	JJ
cord-263987-ff6kor0c	268	15	areas	area	NNS
cord-263987-ff6kor0c	268	16	are	be	VBP
cord-263987-ff6kor0c	268	17	key	key	JJ
cord-263987-ff6kor0c	268	18	to	to	IN
cord-263987-ff6kor0c	268	19	preserving	preserve	VBG
cord-263987-ff6kor0c	268	20	eucalypt	eucalypt	JJ
cord-263987-ff6kor0c	268	21	lineages	lineage	NNS
cord-263987-ff6kor0c	268	22	Identification	identification	NN
cord-263987-ff6kor0c	268	23	of	of	IN
cord-263987-ff6kor0c	268	24	a	a	DT
cord-263987-ff6kor0c	268	25	novel	novel	JJ
cord-263987-ff6kor0c	268	26	coronavirus	coronavirus	NN
cord-263987-ff6kor0c	268	27	in	in	IN
cord-263987-ff6kor0c	268	28	patients	patient	NNS
cord-263987-ff6kor0c	268	29	with	with	IN
cord-263987-ff6kor0c	268	30	severe	severe	JJ
cord-263987-ff6kor0c	268	31	acute	acute	JJ
cord-263987-ff6kor0c	268	32	respiratory	respiratory	JJ
cord-263987-ff6kor0c	268	33	syndrome	syndrome	NN
cord-263987-ff6kor0c	268	34	Bayesian	bayesian	JJ
cord-263987-ff6kor0c	268	35	coalescent	coalescent	JJ
cord-263987-ff6kor0c	268	36	inference	inference	NN
cord-263987-ff6kor0c	268	37	of	of	IN
cord-263987-ff6kor0c	268	38	past	past	JJ
cord-263987-ff6kor0c	268	39	population	population	NN
cord-263987-ff6kor0c	268	40	dynamics	dynamic	NNS
cord-263987-ff6kor0c	268	41	from	from	IN
cord-263987-ff6kor0c	268	42	molecular	molecular	JJ
cord-263987-ff6kor0c	268	43	sequences	sequence	NNS
cord-263987-ff6kor0c	268	44	Unifying	unify	VBG
cord-263987-ff6kor0c	268	45	the	the	DT
cord-263987-ff6kor0c	268	46	spatial	spatial	JJ
cord-263987-ff6kor0c	268	47	epidemiology	epidemiology	NN
cord-263987-ff6kor0c	268	48	and	and	CC
cord-263987-ff6kor0c	268	49	molecular	molecular	JJ
cord-263987-ff6kor0c	268	50	evolution	evolution	NN
cord-263987-ff6kor0c	268	51	of	of	IN
cord-263987-ff6kor0c	269	1	emerging	emerge	VBG
cord-263987-ff6kor0c	269	2	epidemics	epidemic	NNS
cord-263987-ff6kor0c	269	3	Patient	Patient	NNP
cord-263987-ff6kor0c	269	4	0	0	NFP
cord-263987-ff6kor0c	269	5	'	'	''
cord-263987-ff6kor0c	269	6	HIV-1	HIV-1	NNP
cord-263987-ff6kor0c	269	7	genomes	genome	NNS
cord-263987-ff6kor0c	269	8	illuminate	illuminate	VBP
cord-263987-ff6kor0c	269	9	early	early	JJ
cord-263987-ff6kor0c	269	10	HIV	HIV	NNP
cord-263987-ff6kor0c	269	11	/	/	SYM
cord-263987-ff6kor0c	269	12	AIDS	AIDS	NNP
cord-263987-ff6kor0c	269	13	history	history	NN
cord-263987-ff6kor0c	269	14	in	in	IN
cord-263987-ff6kor0c	269	15	North	North	NNP
cord-263987-ff6kor0c	269	16	America	America	NNP
cord-263987-ff6kor0c	270	1	Identifying	identify	VBG
cord-263987-ff6kor0c	270	2	predictors	predictor	NNS
cord-263987-ff6kor0c	270	3	of	of	IN
cord-263987-ff6kor0c	270	4	time	time	NN
cord-263987-ff6kor0c	270	5	-	-	HYPH
cord-263987-ff6kor0c	270	6	inhomogeneous	inhomogeneous	JJ
cord-263987-ff6kor0c	270	7	viral	viral	JJ
cord-263987-ff6kor0c	270	8	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	270	9	processes	process	NNS
cord-263987-ff6kor0c	271	1	A	a	DT
cord-263987-ff6kor0c	271	2	simple	simple	JJ
cord-263987-ff6kor0c	271	3	method	method	NN
cord-263987-ff6kor0c	271	4	for	for	IN
cord-263987-ff6kor0c	271	5	estimating	estimate	VBG
cord-263987-ff6kor0c	271	6	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	271	7	rates	rate	NNS
cord-263987-ff6kor0c	271	8	of	of	IN
cord-263987-ff6kor0c	271	9	base	base	NN
cord-263987-ff6kor0c	271	10	substitutions	substitution	NNS
cord-263987-ff6kor0c	271	11	through	through	IN
cord-263987-ff6kor0c	271	12	comparative	comparative	JJ
cord-263987-ff6kor0c	271	13	studies	study	NNS
cord-263987-ff6kor0c	271	14	of	of	IN
cord-263987-ff6kor0c	271	15	nucleotide	nucleotide	JJ
cord-263987-ff6kor0c	271	16	sequences	sequence	NNS
cord-263987-ff6kor0c	271	17	Dating	date	VBG
cord-263987-ff6kor0c	271	18	the	the	DT
cord-263987-ff6kor0c	271	19	human	human	JJ
cord-263987-ff6kor0c	271	20	-	-	HYPH
cord-263987-ff6kor0c	271	21	ape	ape	NN
cord-263987-ff6kor0c	271	22	splitting	splitting	NN
cord-263987-ff6kor0c	271	23	by	by	IN
cord-263987-ff6kor0c	271	24	a	a	DT
cord-263987-ff6kor0c	271	25	molecular	molecular	JJ
cord-263987-ff6kor0c	271	26	clock	clock	NN
cord-263987-ff6kor0c	271	27	of	of	IN
cord-263987-ff6kor0c	271	28	mitochondrial	mitochondrial	JJ
cord-263987-ff6kor0c	271	29	DNA	DNA	NNP
cord-263987-ff6kor0c	271	30	RevBayes	RevBayes	NNP
cord-263987-ff6kor0c	271	31	:	:	:
cord-263987-ff6kor0c	272	1	Bayesian	bayesian	JJ
cord-263987-ff6kor0c	272	2	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	272	3	inference	inference	NN
cord-263987-ff6kor0c	272	4	using	use	VBG
cord-263987-ff6kor0c	272	5	graphical	graphical	JJ
cord-263987-ff6kor0c	272	6	models	model	NNS
cord-263987-ff6kor0c	272	7	and	and	CC
cord-263987-ff6kor0c	272	8	an	an	DT
cord-263987-ff6kor0c	272	9	interactive	interactive	JJ
cord-263987-ff6kor0c	272	10	model	model	NN
cord-263987-ff6kor0c	272	11	-	-	HYPH
cord-263987-ff6kor0c	272	12	specification	specification	NN
cord-263987-ff6kor0c	272	13	language	language	NN
cord-263987-ff6kor0c	272	14	BEAST	beast	NN
cord-263987-ff6kor0c	272	15	:	:	:
cord-263987-ff6kor0c	273	1	Bayesian	bayesian	JJ
cord-263987-ff6kor0c	273	2	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	273	3	analysis	analysis	NN
cord-263987-ff6kor0c	273	4	by	by	IN
cord-263987-ff6kor0c	273	5	sampling	sampling	NN
cord-263987-ff6kor0c	273	6	trees	tree	NNS
cord-263987-ff6kor0c	273	7	RAxML	RAxML	VBZ
cord-263987-ff6kor0c	273	8	-	-	HYPH
cord-263987-ff6kor0c	273	9	VI	vi	NN
cord-263987-ff6kor0c	273	10	-	-	HYPH
cord-263987-ff6kor0c	273	11	HPC	HPC	NNP
cord-263987-ff6kor0c	273	12	:	:	:
cord-263987-ff6kor0c	273	13	maximum	maximum	JJ
cord-263987-ff6kor0c	273	14	likelihood	likelihood	NN
cord-263987-ff6kor0c	273	15	-	-	HYPH
cord-263987-ff6kor0c	273	16	based	base	VBN
cord-263987-ff6kor0c	273	17	phylogenetic	phylogenetic	NN
cord-263987-ff6kor0c	273	18	analyses	analysis	NNS
cord-263987-ff6kor0c	273	19	with	with	IN
cord-263987-ff6kor0c	273	20	thousands	thousand	NNS
cord-263987-ff6kor0c	273	21	of	of	IN
cord-263987-ff6kor0c	273	22	taxa	taxon	NNS
cord-263987-ff6kor0c	273	23	and	and	CC
cord-263987-ff6kor0c	273	24	mixed	mixed	JJ
cord-263987-ff6kor0c	273	25	models	model	NNS
cord-263987-ff6kor0c	274	1	HyPhy	HyPhy	NNP
cord-263987-ff6kor0c	274	2	:	:	:
cord-263987-ff6kor0c	274	3	hypothesis	hypothesis	NN
cord-263987-ff6kor0c	274	4	testing	testing	NN
cord-263987-ff6kor0c	274	5	using	use	VBG
cord-263987-ff6kor0c	274	6	phylogenies	phylogeny	NNS
cord-263987-ff6kor0c	274	7	PAML	PAML	NNP
cord-263987-ff6kor0c	274	8	4	4	CD
cord-263987-ff6kor0c	274	9	:	:	:
cord-263987-ff6kor0c	274	10	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	274	11	analysis	analysis	NN
cord-263987-ff6kor0c	274	12	by	by	IN
cord-263987-ff6kor0c	274	13	maximum	maximum	JJ
cord-263987-ff6kor0c	274	14	likelihood	likelihood	NN
cord-263987-ff6kor0c	275	1	PHYLIP	PHYLIP	NNP
cord-263987-ff6kor0c	275	2	-phylogeny	-phylogeny	:
cord-263987-ff6kor0c	275	3	inference	inference	NN
cord-263987-ff6kor0c	275	4	package	package	NN
cord-263987-ff6kor0c	275	5	(	(	-LRB-
cord-263987-ff6kor0c	275	6	version	version	NN
cord-263987-ff6kor0c	275	7	3.2	3.2	CD
cord-263987-ff6kor0c	275	8	)	)	-RRB-
cord-263987-ff6kor0c	275	9	TREE	tree	NN
cord-263987-ff6kor0c	275	10	-	-	HYPH
cord-263987-ff6kor0c	275	11	PUZZLE	puzzle	NN
cord-263987-ff6kor0c	275	12	:	:	:
cord-263987-ff6kor0c	275	13	maximum	maximum	JJ
cord-263987-ff6kor0c	275	14	likelihood	likelihood	NN
cord-263987-ff6kor0c	275	15	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	275	16	analysis	analysis	NN
cord-263987-ff6kor0c	275	17	using	use	VBG
cord-263987-ff6kor0c	275	18	quartets	quartet	NNS
cord-263987-ff6kor0c	275	19	and	and	CC
cord-263987-ff6kor0c	275	20	parallel	parallel	NN
cord-263987-ff6kor0c	275	21	computing	computing	NN
cord-263987-ff6kor0c	275	22	Developing	developing	NN
cord-263987-ff6kor0c	275	23	and	and	CC
cord-263987-ff6kor0c	275	24	applying	apply	VBG
cord-263987-ff6kor0c	275	25	heterogeneous	heterogeneous	JJ
cord-263987-ff6kor0c	275	26	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	275	27	models	model	NNS
cord-263987-ff6kor0c	275	28	with	with	IN
cord-263987-ff6kor0c	275	29	XRate	XRate	NNP
cord-263987-ff6kor0c	275	30	Estimation	Estimation	NNP
cord-263987-ff6kor0c	275	31	of	of	IN
cord-263987-ff6kor0c	275	32	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	275	33	distances	distance	NNS
cord-263987-ff6kor0c	275	34	under	under	IN
cord-263987-ff6kor0c	275	35	stationary	stationary	JJ
cord-263987-ff6kor0c	275	36	and	and	CC
cord-263987-ff6kor0c	275	37	nonstationary	nonstationary	JJ
cord-263987-ff6kor0c	275	38	models	model	NNS
cord-263987-ff6kor0c	275	39	of	of	IN
cord-263987-ff6kor0c	275	40	nucleotide	nucleotide	JJ
cord-263987-ff6kor0c	275	41	substitution	substitution	NN
cord-263987-ff6kor0c	275	42	An	an	DT
cord-263987-ff6kor0c	275	43	evolution	evolution	NN
cord-263987-ff6kor0c	275	44	model	model	NN
cord-263987-ff6kor0c	275	45	for	for	IN
cord-263987-ff6kor0c	275	46	sequence	sequence	NN
cord-263987-ff6kor0c	275	47	length	length	NN
cord-263987-ff6kor0c	275	48	based	base	VBN
cord-263987-ff6kor0c	275	49	on	on	IN
cord-263987-ff6kor0c	275	50	residue	residue	NN
cord-263987-ff6kor0c	275	51	insertion	insertion	NN
cord-263987-ff6kor0c	275	52	-	-	HYPH
cord-263987-ff6kor0c	275	53	deletion	deletion	NN
cord-263987-ff6kor0c	275	54	independent	independent	NN
cord-263987-ff6kor0c	275	55	of	of	IN
cord-263987-ff6kor0c	275	56	substitution	substitution	NN
cord-263987-ff6kor0c	275	57	:	:	:
cord-263987-ff6kor0c	275	58	an	an	DT
cord-263987-ff6kor0c	275	59	application	application	NN
cord-263987-ff6kor0c	275	60	to	to	IN
cord-263987-ff6kor0c	275	61	the	the	DT
cord-263987-ff6kor0c	275	62	GC	GC	NNP
cord-263987-ff6kor0c	275	63	content	content	NN
cord-263987-ff6kor0c	275	64	in	in	IN
cord-263987-ff6kor0c	275	65	bacterial	bacterial	JJ
cord-263987-ff6kor0c	275	66	genomes	genome	NNS
cord-263987-ff6kor0c	275	67	A	a	DT
cord-263987-ff6kor0c	275	68	stochastic	stochastic	JJ
cord-263987-ff6kor0c	275	69	gene	gene	NN
cord-263987-ff6kor0c	275	70	evolution	evolution	NN
cord-263987-ff6kor0c	275	71	model	model	NN
cord-263987-ff6kor0c	275	72	with	with	IN
cord-263987-ff6kor0c	275	73	time	time	NN
cord-263987-ff6kor0c	275	74	dependent	dependent	JJ
cord-263987-ff6kor0c	275	75	mutations	mutation	NNS
cord-263987-ff6kor0c	276	1	A	a	DT
cord-263987-ff6kor0c	276	2	nucleotide	nucleotide	JJ
cord-263987-ff6kor0c	276	3	substitution	substitution	NN
cord-263987-ff6kor0c	276	4	model	model	NN
cord-263987-ff6kor0c	276	5	with	with	IN
cord-263987-ff6kor0c	276	6	nearest	near	JJS
cord-263987-ff6kor0c	276	7	-	-	HYPH
cord-263987-ff6kor0c	276	8	neighbour	neighbour	NN
cord-263987-ff6kor0c	276	9	interactions	interaction	NNS
cord-263987-ff6kor0c	277	1	A	a	DT
cord-263987-ff6kor0c	277	2	generalization	generalization	NN
cord-263987-ff6kor0c	277	3	of	of	IN
cord-263987-ff6kor0c	277	4	substitution	substitution	NN
cord-263987-ff6kor0c	277	5	evolution	evolution	NN
cord-263987-ff6kor0c	277	6	models	model	NNS
cord-263987-ff6kor0c	277	7	of	of	IN
cord-263987-ff6kor0c	277	8	nucleotides	nucleotide	NNS
cord-263987-ff6kor0c	277	9	to	to	IN
cord-263987-ff6kor0c	277	10	genetic	genetic	JJ
cord-263987-ff6kor0c	277	11	motifs	motif	NNS
cord-263987-ff6kor0c	277	12	Empirical	empirical	JJ
cord-263987-ff6kor0c	277	13	and	and	CC
cord-263987-ff6kor0c	277	14	structural	structural	JJ
cord-263987-ff6kor0c	277	15	models	model	NNS
cord-263987-ff6kor0c	277	16	for	for	IN
cord-263987-ff6kor0c	277	17	insertions	insertion	NNS
cord-263987-ff6kor0c	277	18	and	and	CC
cord-263987-ff6kor0c	277	19	deletions	deletion	NNS
cord-263987-ff6kor0c	277	20	in	in	IN
cord-263987-ff6kor0c	277	21	the	the	DT
cord-263987-ff6kor0c	277	22	divergent	divergent	JJ
cord-263987-ff6kor0c	277	23	evolution	evolution	NN
cord-263987-ff6kor0c	277	24	of	of	IN
cord-263987-ff6kor0c	277	25	proteins	protein	NNS
cord-263987-ff6kor0c	277	26	Empirical	empirical	JJ
cord-263987-ff6kor0c	277	27	analysis	analysis	NN
cord-263987-ff6kor0c	277	28	of	of	IN
cord-263987-ff6kor0c	277	29	protein	protein	NN
cord-263987-ff6kor0c	277	30	insertions	insertion	NNS
cord-263987-ff6kor0c	277	31	and	and	CC
cord-263987-ff6kor0c	277	32	deletions	deletion	NNS
cord-263987-ff6kor0c	277	33	determining	determine	VBG
cord-263987-ff6kor0c	277	34	parameters	parameter	NNS
cord-263987-ff6kor0c	277	35	for	for	IN
cord-263987-ff6kor0c	277	36	the	the	DT
cord-263987-ff6kor0c	277	37	correct	correct	JJ
cord-263987-ff6kor0c	277	38	placement	placement	NN
cord-263987-ff6kor0c	277	39	of	of	IN
cord-263987-ff6kor0c	277	40	gaps	gap	NNS
cord-263987-ff6kor0c	277	41	in	in	IN
cord-263987-ff6kor0c	277	42	protein	protein	NN
cord-263987-ff6kor0c	277	43	sequence	sequence	NN
cord-263987-ff6kor0c	277	44	alignments	alignment	NNS
cord-263987-ff6kor0c	277	45	Indel	Indel	NNP
cord-263987-ff6kor0c	277	46	PDB	PDB	NNP
cord-263987-ff6kor0c	277	47	:	:	:
cord-263987-ff6kor0c	277	48	a	a	DT
cord-263987-ff6kor0c	277	49	database	database	NN
cord-263987-ff6kor0c	277	50	of	of	IN
cord-263987-ff6kor0c	277	51	structural	structural	JJ
cord-263987-ff6kor0c	277	52	insertions	insertion	NNS
cord-263987-ff6kor0c	277	53	and	and	CC
cord-263987-ff6kor0c	277	54	deletions	deletion	NNS
cord-263987-ff6kor0c	277	55	derived	derive	VBN
cord-263987-ff6kor0c	277	56	from	from	IN
cord-263987-ff6kor0c	277	57	sequence	sequence	NN
cord-263987-ff6kor0c	277	58	alignments	alignment	NNS
cord-263987-ff6kor0c	277	59	of	of	IN
cord-263987-ff6kor0c	277	60	closely	closely	RB
cord-263987-ff6kor0c	277	61	related	related	JJ
cord-263987-ff6kor0c	277	62	proteins	protein	NNS
cord-263987-ff6kor0c	277	63	Sequence	sequence	NN
cord-263987-ff6kor0c	277	64	context	context	NN
cord-263987-ff6kor0c	277	65	of	of	IN
cord-263987-ff6kor0c	277	66	indel	indel	NN
cord-263987-ff6kor0c	277	67	mutations	mutation	NNS
cord-263987-ff6kor0c	277	68	and	and	CC
cord-263987-ff6kor0c	277	69	their	-PRON-	PRP$
cord-263987-ff6kor0c	277	70	effect	effect	NN
cord-263987-ff6kor0c	277	71	on	on	IN
cord-263987-ff6kor0c	277	72	protein	protein	NN
cord-263987-ff6kor0c	277	73	evolution	evolution	NN
cord-263987-ff6kor0c	277	74	in	in	IN
cord-263987-ff6kor0c	277	75	a	a	DT
cord-263987-ff6kor0c	277	76	bacterial	bacterial	JJ
cord-263987-ff6kor0c	277	77	endosymbiont	endosymbiont	NN
cord-263987-ff6kor0c	277	78	Alignment	Alignment	NNP
cord-263987-ff6kor0c	277	79	of	of	IN
cord-263987-ff6kor0c	277	80	phylogenetically	phylogenetically	RB
cord-263987-ff6kor0c	277	81	unambiguous	unambiguous	JJ
cord-263987-ff6kor0c	277	82	indels	indel	NNS
cord-263987-ff6kor0c	277	83	in	in	IN
cord-263987-ff6kor0c	277	84	Shewanella	Shewanella	NNP
cord-263987-ff6kor0c	277	85	Identification	Identification	NNP
cord-263987-ff6kor0c	277	86	of	of	IN
cord-263987-ff6kor0c	277	87	transposable	transposable	JJ
cord-263987-ff6kor0c	277	88	elements	element	NNS
cord-263987-ff6kor0c	277	89	using	use	VBG
cord-263987-ff6kor0c	277	90	multiple	multiple	JJ
cord-263987-ff6kor0c	277	91	alignments	alignment	NNS
cord-263987-ff6kor0c	277	92	of	of	IN
cord-263987-ff6kor0c	277	93	related	related	JJ
cord-263987-ff6kor0c	277	94	genomes	genome	NNS
cord-263987-ff6kor0c	277	95	Statistical	statistical	JJ
cord-263987-ff6kor0c	277	96	alignment	alignment	NN
cord-263987-ff6kor0c	277	97	:	:	:
cord-263987-ff6kor0c	277	98	computational	computational	JJ
cord-263987-ff6kor0c	277	99	properties	property	NNS
cord-263987-ff6kor0c	277	100	,	,	,
cord-263987-ff6kor0c	277	101	homology	homology	NN
cord-263987-ff6kor0c	277	102	testing	testing	NN
cord-263987-ff6kor0c	277	103	and	and	CC
cord-263987-ff6kor0c	277	104	goodness	goodness	NN
cord-263987-ff6kor0c	277	105	-	-	HYPH
cord-263987-ff6kor0c	277	106	of	of	IN
cord-263987-ff6kor0c	277	107	-	-	HYPH
cord-263987-ff6kor0c	277	108	fit	fit	JJ
cord-263987-ff6kor0c	277	109	General	General	NNP
cord-263987-ff6kor0c	277	110	continuous	continuous	JJ
cord-263987-ff6kor0c	277	111	-	-	HYPH
cord-263987-ff6kor0c	277	112	time	time	NN
cord-263987-ff6kor0c	277	113	Markov	Markov	NNP
cord-263987-ff6kor0c	277	114	model	model	NN
cord-263987-ff6kor0c	277	115	of	of	IN
cord-263987-ff6kor0c	277	116	sequence	sequence	NN
cord-263987-ff6kor0c	277	117	evolution	evolution	NN
cord-263987-ff6kor0c	277	118	via	via	IN
cord-263987-ff6kor0c	277	119	insertions	insertion	NNS
cord-263987-ff6kor0c	277	120	/	/	SYM
cord-263987-ff6kor0c	277	121	deletions	deletion	NNS
cord-263987-ff6kor0c	277	122	:	:	:
cord-263987-ff6kor0c	277	123	are	be	VBP
cord-263987-ff6kor0c	277	124	alignment	alignment	NN
cord-263987-ff6kor0c	277	125	probabilities	probability	NNS
cord-263987-ff6kor0c	277	126	factorable	factorable	JJ
cord-263987-ff6kor0c	277	127	?	?	.
cord-263987-ff6kor0c	278	1	General	general	JJ
cord-263987-ff6kor0c	278	2	continuous	continuous	JJ
cord-263987-ff6kor0c	278	3	-	-	HYPH
cord-263987-ff6kor0c	278	4	time	time	NN
cord-263987-ff6kor0c	278	5	Markov	Markov	NNP
cord-263987-ff6kor0c	278	6	model	model	NN
cord-263987-ff6kor0c	278	7	of	of	IN
cord-263987-ff6kor0c	278	8	sequence	sequence	NN
cord-263987-ff6kor0c	278	9	evolution	evolution	NN
cord-263987-ff6kor0c	278	10	via	via	IN
cord-263987-ff6kor0c	278	11	insertions	insertion	NNS
cord-263987-ff6kor0c	278	12	/	/	SYM
cord-263987-ff6kor0c	278	13	deletions	deletion	NNS
cord-263987-ff6kor0c	278	14	:	:	:
cord-263987-ff6kor0c	278	15	local	local	JJ
cord-263987-ff6kor0c	278	16	alignment	alignment	NN
cord-263987-ff6kor0c	278	17	probability	probability	NN
cord-263987-ff6kor0c	278	18	computation	computation	NN
cord-263987-ff6kor0c	278	19	Erratum	Erratum	NNP
cord-263987-ff6kor0c	278	20	to	to	IN
cord-263987-ff6kor0c	278	21	:	:	:
cord-263987-ff6kor0c	278	22	General	general	JJ
cord-263987-ff6kor0c	278	23	continuous	continuous	JJ
cord-263987-ff6kor0c	278	24	-	-	HYPH
cord-263987-ff6kor0c	278	25	time	time	NN
cord-263987-ff6kor0c	278	26	Markov	Markov	NNP
cord-263987-ff6kor0c	278	27	model	model	NN
cord-263987-ff6kor0c	278	28	of	of	IN
cord-263987-ff6kor0c	278	29	sequence	sequence	NN
cord-263987-ff6kor0c	278	30	evolution	evolution	NN
cord-263987-ff6kor0c	278	31	via	via	IN
cord-263987-ff6kor0c	278	32	insertions	insertion	NNS
cord-263987-ff6kor0c	278	33	/	/	SYM
cord-263987-ff6kor0c	278	34	deletions	deletion	NNS
cord-263987-ff6kor0c	278	35	:	:	:
cord-263987-ff6kor0c	278	36	are	be	VBP
cord-263987-ff6kor0c	278	37	alignment	alignment	NN
cord-263987-ff6kor0c	278	38	probabilities	probability	NNS
cord-263987-ff6kor0c	278	39	factorable	factorable	JJ
cord-263987-ff6kor0c	278	40	?	?	.
cord-263987-ff6kor0c	279	1	Parameterizing	parameterizing	NN
cord-263987-ff6kor0c	279	2	sequence	sequence	NN
cord-263987-ff6kor0c	279	3	alignment	alignment	NN
cord-263987-ff6kor0c	279	4	with	with	IN
cord-263987-ff6kor0c	279	5	an	an	DT
cord-263987-ff6kor0c	279	6	explicit	explicit	JJ
cord-263987-ff6kor0c	279	7	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	279	8	model	model	NN
cord-263987-ff6kor0c	279	9	Multiple	multiple	JJ
cord-263987-ff6kor0c	279	10	genome	genome	NN
cord-263987-ff6kor0c	279	11	rearrangement	rearrangement	NN
cord-263987-ff6kor0c	279	12	and	and	CC
cord-263987-ff6kor0c	279	13	breakpoint	breakpoint	NN
cord-263987-ff6kor0c	279	14	phylogeny	phylogeny	NN
cord-263987-ff6kor0c	279	15	Analytical	analytical	JJ
cord-263987-ff6kor0c	279	16	expression	expression	NN
cord-263987-ff6kor0c	279	17	of	of	IN
cord-263987-ff6kor0c	279	18	the	the	DT
cord-263987-ff6kor0c	279	19	purine	purine	NNP
cord-263987-ff6kor0c	279	20	/	/	SYM
cord-263987-ff6kor0c	279	21	pyrimidine	pyrimidine	NN
cord-263987-ff6kor0c	279	22	codon	codon	NN
cord-263987-ff6kor0c	279	23	probability	probability	NN
cord-263987-ff6kor0c	279	24	after	after	IN
cord-263987-ff6kor0c	279	25	and	and	CC
cord-263987-ff6kor0c	279	26	before	before	IN
cord-263987-ff6kor0c	279	27	random	random	JJ
cord-263987-ff6kor0c	279	28	mutations	mutation	NNS
cord-263987-ff6kor0c	280	1	Analytical	analytical	JJ
cord-263987-ff6kor0c	280	2	solutions	solution	NNS
cord-263987-ff6kor0c	280	3	of	of	IN
cord-263987-ff6kor0c	280	4	the	the	DT
cord-263987-ff6kor0c	280	5	dinucleotide	dinucleotide	NN
cord-263987-ff6kor0c	280	6	probability	probability	NN
cord-263987-ff6kor0c	280	7	after	after	IN
cord-263987-ff6kor0c	280	8	and	and	CC
cord-263987-ff6kor0c	280	9	before	before	IN
cord-263987-ff6kor0c	280	10	random	random	JJ
cord-263987-ff6kor0c	280	11	mutations	mutation	NNS
cord-263987-ff6kor0c	281	1	RNA	RNA	NNP
cord-263987-ff6kor0c	281	2	secondary	secondary	JJ
cord-263987-ff6kor0c	281	3	structure	structure	NN
cord-263987-ff6kor0c	281	4	prediction	prediction	NN
cord-263987-ff6kor0c	281	5	using	use	VBG
cord-263987-ff6kor0c	281	6	stochastic	stochastic	JJ
cord-263987-ff6kor0c	281	7	context	context	NN
cord-263987-ff6kor0c	281	8	-	-	HYPH
cord-263987-ff6kor0c	281	9	free	free	JJ
cord-263987-ff6kor0c	281	10	grammars	grammar	NNS
cord-263987-ff6kor0c	281	11	and	and	CC
cord-263987-ff6kor0c	281	12	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	281	13	history	history	NN
cord-263987-ff6kor0c	282	1	Evolution	evolution	NN
cord-263987-ff6kor0c	282	2	probabilities	probability	NNS
cord-263987-ff6kor0c	282	3	and	and	CC
cord-263987-ff6kor0c	282	4	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	282	5	distance	distance	NN
cord-263987-ff6kor0c	282	6	of	of	IN
cord-263987-ff6kor0c	282	7	dinucleotides	dinucleotides	NNP
cord-263987-ff6kor0c	282	8	Genome	Genome	NNP
cord-263987-ff6kor0c	282	9	evolution	evolution	NN
cord-263987-ff6kor0c	282	10	by	by	IN
cord-263987-ff6kor0c	282	11	transformation	transformation	NN
cord-263987-ff6kor0c	282	12	,	,	,
cord-263987-ff6kor0c	282	13	expansion	expansion	NN
cord-263987-ff6kor0c	282	14	and	and	CC
cord-263987-ff6kor0c	282	15	contraction	contraction	NN
cord-263987-ff6kor0c	282	16	(	(	-LRB-
cord-263987-ff6kor0c	282	17	GETEC	GETEC	NNP
cord-263987-ff6kor0c	282	18	)	)	-RRB-
cord-263987-ff6kor0c	283	1	An	an	DT
cord-263987-ff6kor0c	283	2	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	283	3	model	model	NN
cord-263987-ff6kor0c	283	4	for	for	IN
cord-263987-ff6kor0c	283	5	maximum	maximum	JJ
cord-263987-ff6kor0c	283	6	likelihood	likelihood	NN
cord-263987-ff6kor0c	283	7	alignment	alignment	NN
cord-263987-ff6kor0c	283	8	of	of	IN
cord-263987-ff6kor0c	283	9	DNA	dna	NN
cord-263987-ff6kor0c	283	10	sequences	sequence	NNS
cord-263987-ff6kor0c	284	1	An	an	DT
cord-263987-ff6kor0c	284	2	introduction	introduction	NN
cord-263987-ff6kor0c	284	3	to	to	IN
cord-263987-ff6kor0c	284	4	probability	probability	NN
cord-263987-ff6kor0c	284	5	theory	theory	NN
cord-263987-ff6kor0c	284	6	and	and	CC
cord-263987-ff6kor0c	284	7	its	-PRON-	PRP$
cord-263987-ff6kor0c	284	8	applications	application	NNS
cord-263987-ff6kor0c	284	9	Evolutionary	Evolutionary	NNP
cord-263987-ff6kor0c	284	10	HMMs	HMMs	NNPS
cord-263987-ff6kor0c	284	11	:	:	:
cord-263987-ff6kor0c	284	12	a	a	DT
cord-263987-ff6kor0c	284	13	Bayesian	bayesian	JJ
cord-263987-ff6kor0c	284	14	approach	approach	NN
cord-263987-ff6kor0c	284	15	to	to	IN
cord-263987-ff6kor0c	284	16	multiple	multiple	JJ
cord-263987-ff6kor0c	284	17	alignment	alignment	NN
cord-263987-ff6kor0c	284	18	Using	use	VBG
cord-263987-ff6kor0c	284	19	guide	guide	NN
cord-263987-ff6kor0c	284	20	trees	tree	NNS
cord-263987-ff6kor0c	284	21	to	to	TO
cord-263987-ff6kor0c	284	22	construct	construct	VB
cord-263987-ff6kor0c	284	23	multiple	multiple	JJ
cord-263987-ff6kor0c	284	24	-	-	HYPH
cord-263987-ff6kor0c	284	25	sequence	sequence	NN
cord-263987-ff6kor0c	284	26	evolutionary	evolutionary	NN
cord-263987-ff6kor0c	284	27	HMMs	HMMs	NNPS
cord-263987-ff6kor0c	285	1	Accurate	accurate	JJ
cord-263987-ff6kor0c	285	2	reconstruction	reconstruction	NN
cord-263987-ff6kor0c	285	3	of	of	IN
cord-263987-ff6kor0c	285	4	insertion	insertion	NN
cord-263987-ff6kor0c	285	5	-	-	HYPH
cord-263987-ff6kor0c	285	6	deletion	deletion	NN
cord-263987-ff6kor0c	285	7	histories	history	NNS
cord-263987-ff6kor0c	285	8	by	by	IN
cord-263987-ff6kor0c	285	9	statistical	statistical	JJ
cord-263987-ff6kor0c	285	10	phylogenetics	phylogenetic	NNS
cord-263987-ff6kor0c	286	1	A	a	DT
cord-263987-ff6kor0c	286	2	note	note	NN
cord-263987-ff6kor0c	286	3	on	on	IN
cord-263987-ff6kor0c	286	4	probabilistic	probabilistic	JJ
cord-263987-ff6kor0c	286	5	models	model	NNS
cord-263987-ff6kor0c	286	6	over	over	IN
cord-263987-ff6kor0c	286	7	strings	string	NNS
cord-263987-ff6kor0c	286	8	:	:	:
cord-263987-ff6kor0c	286	9	the	the	DT
cord-263987-ff6kor0c	286	10	linear	linear	JJ
cord-263987-ff6kor0c	286	11	algebra	algebra	NN
cord-263987-ff6kor0c	286	12	approach	approach	NN
cord-263987-ff6kor0c	286	13	Statistical	statistical	JJ
cord-263987-ff6kor0c	286	14	alignment	alignment	NN
cord-263987-ff6kor0c	286	15	based	base	VBN
cord-263987-ff6kor0c	286	16	on	on	IN
cord-263987-ff6kor0c	286	17	fragment	fragment	NN
cord-263987-ff6kor0c	286	18	insertion	insertion	NN
cord-263987-ff6kor0c	286	19	and	and	CC
cord-263987-ff6kor0c	286	20	deletion	deletion	NN
cord-263987-ff6kor0c	286	21	models	model	NNS
cord-263987-ff6kor0c	286	22	Evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	286	23	inference	inference	NN
cord-263987-ff6kor0c	286	24	via	via	IN
cord-263987-ff6kor0c	286	25	the	the	DT
cord-263987-ff6kor0c	286	26	poisson	poisson	NNP
cord-263987-ff6kor0c	286	27	indel	indel	NNP
cord-263987-ff6kor0c	286	28	process	process	NN
cord-263987-ff6kor0c	286	29	Inching	inch	VBG
cord-263987-ff6kor0c	286	30	toward	toward	IN
cord-263987-ff6kor0c	286	31	reality	reality	NN
cord-263987-ff6kor0c	286	32	:	:	:
cord-263987-ff6kor0c	286	33	an	an	DT
cord-263987-ff6kor0c	286	34	improved	improved	JJ
cord-263987-ff6kor0c	286	35	likelihood	likelihood	NN
cord-263987-ff6kor0c	286	36	model	model	NN
cord-263987-ff6kor0c	286	37	of	of	IN
cord-263987-ff6kor0c	286	38	sequence	sequence	NN
cord-263987-ff6kor0c	286	39	evolution	evolution	NN
cord-263987-ff6kor0c	286	40	Models	model	NNS
cord-263987-ff6kor0c	286	41	of	of	IN
cord-263987-ff6kor0c	286	42	sequence	sequence	NN
cord-263987-ff6kor0c	286	43	evolution	evolution	NN
cord-263987-ff6kor0c	286	44	for	for	IN
cord-263987-ff6kor0c	286	45	DNA	dna	NN
cord-263987-ff6kor0c	286	46	sequences	sequence	NNS
cord-263987-ff6kor0c	286	47	containing	contain	VBG
cord-263987-ff6kor0c	286	48	gaps	gap	NNS
cord-263987-ff6kor0c	286	49	Evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	286	50	models	model	NNS
cord-263987-ff6kor0c	286	51	for	for	IN
cord-263987-ff6kor0c	286	52	insertions	insertion	NNS
cord-263987-ff6kor0c	286	53	and	and	CC
cord-263987-ff6kor0c	286	54	deletions	deletion	NNS
cord-263987-ff6kor0c	286	55	in	in	IN
cord-263987-ff6kor0c	286	56	a	a	DT
cord-263987-ff6kor0c	286	57	probabilistic	probabilistic	JJ
cord-263987-ff6kor0c	286	58	modeling	modeling	NN
cord-263987-ff6kor0c	286	59	framework	framework	NN
cord-263987-ff6kor0c	286	60	Probabilistic	probabilistic	JJ
cord-263987-ff6kor0c	286	61	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	286	62	inference	inference	NN
cord-263987-ff6kor0c	286	63	with	with	IN
cord-263987-ff6kor0c	286	64	insertions	insertion	NNS
cord-263987-ff6kor0c	286	65	and	and	CC
cord-263987-ff6kor0c	286	66	deletions	deletion	NNS
cord-263987-ff6kor0c	286	67	A	a	DT
cord-263987-ff6kor0c	286	68	probabilistic	probabilistic	JJ
cord-263987-ff6kor0c	286	69	model	model	NN
cord-263987-ff6kor0c	286	70	for	for	IN
cord-263987-ff6kor0c	286	71	the	the	DT
cord-263987-ff6kor0c	286	72	evolution	evolution	NN
cord-263987-ff6kor0c	286	73	of	of	IN
cord-263987-ff6kor0c	286	74	RNA	RNA	NNP
cord-263987-ff6kor0c	286	75	structure	structure	NN
cord-263987-ff6kor0c	286	76	Pair	pair	NN
cord-263987-ff6kor0c	286	77	stochastic	stochastic	JJ
cord-263987-ff6kor0c	286	78	tree	tree	NN
cord-263987-ff6kor0c	286	79	adjoining	adjoin	VBG
cord-263987-ff6kor0c	286	80	grammars	grammar	NNS
cord-263987-ff6kor0c	286	81	for	for	IN
cord-263987-ff6kor0c	286	82	aligning	align	VBG
cord-263987-ff6kor0c	286	83	and	and	CC
cord-263987-ff6kor0c	286	84	predicting	predict	VBG
cord-263987-ff6kor0c	286	85	pseudoknot	pseudoknot	NNP
cord-263987-ff6kor0c	286	86	RNA	RNA	NNP
cord-263987-ff6kor0c	286	87	structures	structure	NNS
cord-263987-ff6kor0c	287	1	A	a	DT
cord-263987-ff6kor0c	287	2	probabilistic	probabilistic	JJ
cord-263987-ff6kor0c	287	3	model	model	NN
cord-263987-ff6kor0c	287	4	for	for	IN
cord-263987-ff6kor0c	287	5	sequence	sequence	NN
cord-263987-ff6kor0c	287	6	alignment	alignment	NN
cord-263987-ff6kor0c	287	7	with	with	IN
cord-263987-ff6kor0c	287	8	context	context	NN
cord-263987-ff6kor0c	287	9	-	-	HYPH
cord-263987-ff6kor0c	287	10	sensitive	sensitive	JJ
cord-263987-ff6kor0c	287	11	indels	indel	NNS
cord-263987-ff6kor0c	287	12	Sequence	sequence	NN
cord-263987-ff6kor0c	287	13	alignments	alignment	NNS
cord-263987-ff6kor0c	287	14	and	and	CC
cord-263987-ff6kor0c	287	15	pair	pair	VBP
cord-263987-ff6kor0c	287	16	hidden	hide	VBN
cord-263987-ff6kor0c	287	17	Markov	Markov	NNP
cord-263987-ff6kor0c	287	18	models	model	NNS
cord-263987-ff6kor0c	287	19	using	use	VBG
cord-263987-ff6kor0c	287	20	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	287	21	history	history	NN
cord-263987-ff6kor0c	287	22	Joint	joint	JJ
cord-263987-ff6kor0c	287	23	Bayesian	bayesian	JJ
cord-263987-ff6kor0c	287	24	estimation	estimation	NN
cord-263987-ff6kor0c	287	25	of	of	IN
cord-263987-ff6kor0c	287	26	alignment	alignment	NN
cord-263987-ff6kor0c	287	27	and	and	CC
cord-263987-ff6kor0c	287	28	phylogeny	phylogeny	NN
cord-263987-ff6kor0c	287	29	BAli	BAli	NNP
cord-263987-ff6kor0c	287	30	-	-	HYPH
cord-263987-ff6kor0c	287	31	Phy	Phy	NNP
cord-263987-ff6kor0c	287	32	:	:	:
cord-263987-ff6kor0c	287	33	simultaneous	simultaneous	JJ
cord-263987-ff6kor0c	287	34	Bayesian	bayesian	JJ
cord-263987-ff6kor0c	287	35	inference	inference	NN
cord-263987-ff6kor0c	287	36	of	of	IN
cord-263987-ff6kor0c	287	37	alignment	alignment	NN
cord-263987-ff6kor0c	287	38	and	and	CC
cord-263987-ff6kor0c	287	39	phylogeny	phylogeny	NN
cord-263987-ff6kor0c	288	1	Incorporating	incorporate	VBG
cord-263987-ff6kor0c	288	2	indel	indel	NN
cord-263987-ff6kor0c	288	3	information	information	NN
cord-263987-ff6kor0c	288	4	into	into	IN
cord-263987-ff6kor0c	288	5	phylogeny	phylogeny	NN
cord-263987-ff6kor0c	288	6	estimation	estimation	NN
cord-263987-ff6kor0c	288	7	for	for	IN
cord-263987-ff6kor0c	288	8	rapidly	rapidly	RB
cord-263987-ff6kor0c	288	9	emerging	emerge	VBG
cord-263987-ff6kor0c	288	10	pathogens	pathogen	NNS
cord-263987-ff6kor0c	288	11	Phylogenetic	Phylogenetic	NNP
cord-263987-ff6kor0c	288	12	automata	automata	NN
cord-263987-ff6kor0c	288	13	,	,	,
cord-263987-ff6kor0c	288	14	pruning	pruning	NN
cord-263987-ff6kor0c	288	15	,	,	,
cord-263987-ff6kor0c	288	16	and	and	CC
cord-263987-ff6kor0c	288	17	multiple	multiple	JJ
cord-263987-ff6kor0c	288	18	alignment	alignment	NN
cord-263987-ff6kor0c	288	19	Hand	hand	NN
cord-263987-ff6kor0c	288	20	Align	Align	NNP
cord-263987-ff6kor0c	288	21	:	:	:
cord-263987-ff6kor0c	288	22	Bayesian	bayesian	JJ
cord-263987-ff6kor0c	288	23	multiple	multiple	JJ
cord-263987-ff6kor0c	288	24	sequence	sequence	NN
cord-263987-ff6kor0c	288	25	alignment	alignment	NN
cord-263987-ff6kor0c	288	26	,	,	,
cord-263987-ff6kor0c	288	27	phylogeny	phylogeny	NN
cord-263987-ff6kor0c	288	28	,	,	,
cord-263987-ff6kor0c	288	29	and	and	CC
cord-263987-ff6kor0c	288	30	ancestral	ancestral	JJ
cord-263987-ff6kor0c	288	31	reconstruction	reconstruction	NN
cord-263987-ff6kor0c	289	1	A	a	DT
cord-263987-ff6kor0c	289	2	long	long	JJ
cord-263987-ff6kor0c	289	3	indel	indel	NN
cord-263987-ff6kor0c	289	4	model	model	NN
cord-263987-ff6kor0c	289	5	for	for	IN
cord-263987-ff6kor0c	289	6	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	289	7	sequence	sequence	NN
cord-263987-ff6kor0c	289	8	alignment	alignment	NN
cord-263987-ff6kor0c	289	9	An	an	DT
cord-263987-ff6kor0c	289	10	improved	improved	JJ
cord-263987-ff6kor0c	289	11	model	model	NN
cord-263987-ff6kor0c	289	12	for	for	IN
cord-263987-ff6kor0c	289	13	statistical	statistical	JJ
cord-263987-ff6kor0c	289	14	alignment	alignment	NN
cord-263987-ff6kor0c	289	15	Chain	Chain	NNP
cord-263987-ff6kor0c	289	16	Monte	Monte	NNP
cord-263987-ff6kor0c	289	17	Carlo	Carlo	NNP
cord-263987-ff6kor0c	289	18	Expectation	Expectation	NNP
cord-263987-ff6kor0c	289	19	Maximization	Maximization	NNP
cord-263987-ff6kor0c	289	20	algorithm	algorithm	NN
cord-263987-ff6kor0c	289	21	for	for	IN
cord-263987-ff6kor0c	289	22	statistical	statistical	JJ
cord-263987-ff6kor0c	289	23	analysis	analysis	NN
cord-263987-ff6kor0c	289	24	of	of	IN
cord-263987-ff6kor0c	289	25	DNA	dna	NN
cord-263987-ff6kor0c	289	26	sequence	sequence	NN
cord-263987-ff6kor0c	289	27	evolution	evolution	NN
cord-263987-ff6kor0c	289	28	with	with	IN
cord-263987-ff6kor0c	289	29	neighbor	neighbor	NN
cord-263987-ff6kor0c	289	30	-	-	HYPH
cord-263987-ff6kor0c	289	31	dependent	dependent	JJ
cord-263987-ff6kor0c	289	32	substitution	substitution	NN
cord-263987-ff6kor0c	289	33	rates	rate	NNS
cord-263987-ff6kor0c	290	1	Accurate	accurate	JJ
cord-263987-ff6kor0c	290	2	estimation	estimation	NN
cord-263987-ff6kor0c	290	3	of	of	IN
cord-263987-ff6kor0c	290	4	substitution	substitution	NN
cord-263987-ff6kor0c	290	5	rates	rate	NNS
cord-263987-ff6kor0c	290	6	with	with	IN
cord-263987-ff6kor0c	290	7	neighbor	neighbor	NN
cord-263987-ff6kor0c	290	8	-	-	HYPH
cord-263987-ff6kor0c	290	9	dependent	dependent	JJ
cord-263987-ff6kor0c	290	10	models	model	NNS
cord-263987-ff6kor0c	290	11	in	in	IN
cord-263987-ff6kor0c	290	12	a	a	DT
cord-263987-ff6kor0c	290	13	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	290	14	context	context	NN
cord-263987-ff6kor0c	290	15	Patterns	pattern	NNS
cord-263987-ff6kor0c	290	16	of	of	IN
cord-263987-ff6kor0c	290	17	insertion	insertion	NN
cord-263987-ff6kor0c	290	18	and	and	CC
cord-263987-ff6kor0c	290	19	deletion	deletion	NN
cord-263987-ff6kor0c	290	20	in	in	IN
cord-263987-ff6kor0c	290	21	mammalian	mammalian	JJ
cord-263987-ff6kor0c	290	22	genomes	genome	NNS
cord-263987-ff6kor0c	290	23	Exhaustive	exhaustive	JJ
cord-263987-ff6kor0c	290	24	matching	matching	NN
cord-263987-ff6kor0c	290	25	of	of	IN
cord-263987-ff6kor0c	290	26	the	the	DT
cord-263987-ff6kor0c	290	27	entire	entire	JJ
cord-263987-ff6kor0c	290	28	protein	protein	NN
cord-263987-ff6kor0c	290	29	sequence	sequence	NN
cord-263987-ff6kor0c	290	30	database	database	NN
cord-263987-ff6kor0c	290	31	Pattern	pattern	NN
cord-263987-ff6kor0c	290	32	and	and	CC
cord-263987-ff6kor0c	290	33	rate	rate	NN
cord-263987-ff6kor0c	290	34	of	of	IN
cord-263987-ff6kor0c	290	35	indel	indel	NN
cord-263987-ff6kor0c	290	36	evolution	evolution	NN
cord-263987-ff6kor0c	290	37	inferred	infer	VBN
cord-263987-ff6kor0c	290	38	from	from	IN
cord-263987-ff6kor0c	290	39	whole	whole	JJ
cord-263987-ff6kor0c	290	40	chloroplast	chloroplast	NN
cord-263987-ff6kor0c	290	41	intergenic	intergenic	JJ
cord-263987-ff6kor0c	290	42	regions	region	NNS
cord-263987-ff6kor0c	290	43	in	in	IN
cord-263987-ff6kor0c	290	44	sugarcane	sugarcane	NN
cord-263987-ff6kor0c	290	45	,	,	,
cord-263987-ff6kor0c	290	46	maize	maize	NN
cord-263987-ff6kor0c	290	47	and	and	CC
cord-263987-ff6kor0c	290	48	rice	rice	NN
cord-263987-ff6kor0c	290	49	Patterns	pattern	NNS
cord-263987-ff6kor0c	290	50	of	of	IN
cord-263987-ff6kor0c	290	51	nucleotide	nucleotide	JJ
cord-263987-ff6kor0c	290	52	substitution	substitution	NN
cord-263987-ff6kor0c	290	53	,	,	,
cord-263987-ff6kor0c	290	54	insertion	insertion	NN
cord-263987-ff6kor0c	290	55	and	and	CC
cord-263987-ff6kor0c	290	56	deletion	deletion	NN
cord-263987-ff6kor0c	290	57	in	in	IN
cord-263987-ff6kor0c	290	58	the	the	DT
cord-263987-ff6kor0c	290	59	human	human	JJ
cord-263987-ff6kor0c	290	60	genome	genome	NN
cord-263987-ff6kor0c	290	61	inferred	infer	VBN
cord-263987-ff6kor0c	290	62	from	from	IN
cord-263987-ff6kor0c	290	63	pseudogenes	pseudogene	NNS
cord-263987-ff6kor0c	290	64	The	the	DT
cord-263987-ff6kor0c	290	65	size	size	NN
cord-263987-ff6kor0c	290	66	distribution	distribution	NN
cord-263987-ff6kor0c	290	67	of	of	IN
cord-263987-ff6kor0c	290	68	insertions	insertion	NNS
cord-263987-ff6kor0c	290	69	and	and	CC
cord-263987-ff6kor0c	290	70	deletions	deletion	NNS
cord-263987-ff6kor0c	290	71	in	in	IN
cord-263987-ff6kor0c	290	72	human	human	JJ
cord-263987-ff6kor0c	290	73	and	and	CC
cord-263987-ff6kor0c	290	74	rodent	rodent	NN
cord-263987-ff6kor0c	290	75	pseudogenes	pseudogene	NNS
cord-263987-ff6kor0c	290	76	suggests	suggest	VBZ
cord-263987-ff6kor0c	290	77	the	the	DT
cord-263987-ff6kor0c	290	78	logarithmic	logarithmic	JJ
cord-263987-ff6kor0c	290	79	gap	gap	NN
cord-263987-ff6kor0c	290	80	penalty	penalty	NN
cord-263987-ff6kor0c	290	81	for	for	IN
cord-263987-ff6kor0c	290	82	sequence	sequence	NN
cord-263987-ff6kor0c	290	83	alignment	alignment	NN
cord-263987-ff6kor0c	290	84	Problems	problem	NNS
cord-263987-ff6kor0c	290	85	and	and	CC
cord-263987-ff6kor0c	290	86	solutions	solution	NNS
cord-263987-ff6kor0c	290	87	for	for	IN
cord-263987-ff6kor0c	290	88	estimating	estimate	VBG
cord-263987-ff6kor0c	290	89	indel	indel	NN
cord-263987-ff6kor0c	290	90	rates	rate	NNS
cord-263987-ff6kor0c	290	91	and	and	CC
cord-263987-ff6kor0c	290	92	length	length	NN
cord-263987-ff6kor0c	290	93	distributions	distribution	NNS
cord-263987-ff6kor0c	290	94	Uncertainty	uncertainty	NN
cord-263987-ff6kor0c	290	95	in	in	IN
cord-263987-ff6kor0c	290	96	homology	homology	NN
cord-263987-ff6kor0c	290	97	inferences	inference	NNS
cord-263987-ff6kor0c	290	98	:	:	:
cord-263987-ff6kor0c	290	99	assessing	assess	VBG
cord-263987-ff6kor0c	290	100	and	and	CC
cord-263987-ff6kor0c	290	101	improving	improve	VBG
cord-263987-ff6kor0c	290	102	genomic	genomic	JJ
cord-263987-ff6kor0c	290	103	sequence	sequence	NN
cord-263987-ff6kor0c	290	104	alignment	alignment	NN
cord-263987-ff6kor0c	290	105	Sequence	sequence	NN
cord-263987-ff6kor0c	290	106	comparison	comparison	NN
cord-263987-ff6kor0c	290	107	with	with	IN
cord-263987-ff6kor0c	290	108	concave	concave	JJ
cord-263987-ff6kor0c	290	109	weighting	weighting	NN
cord-263987-ff6kor0c	290	110	functions	function	NNS
cord-263987-ff6kor0c	290	111	Probabilistic	probabilistic	JJ
cord-263987-ff6kor0c	290	112	consistency	consistency	NN
cord-263987-ff6kor0c	290	113	-	-	HYPH
cord-263987-ff6kor0c	290	114	based	base	VBN
cord-263987-ff6kor0c	290	115	multiple	multiple	JJ
cord-263987-ff6kor0c	290	116	sequence	sequence	NN
cord-263987-ff6kor0c	290	117	alignment	alignment	NN
cord-263987-ff6kor0c	290	118	Prediction	Prediction	NNP
cord-263987-ff6kor0c	290	119	of	of	IN
cord-263987-ff6kor0c	290	120	complete	complete	JJ
cord-263987-ff6kor0c	290	121	gene	gene	NN
cord-263987-ff6kor0c	290	122	structures	structure	NNS
cord-263987-ff6kor0c	290	123	in	in	IN
cord-263987-ff6kor0c	290	124	human	human	JJ
cord-263987-ff6kor0c	290	125	genomic	genomic	NN
cord-263987-ff6kor0c	290	126	DNA	DNA	NNP
cord-263987-ff6kor0c	290	127	Indelign	Indelign	NNP
cord-263987-ff6kor0c	290	128	:	:	:
cord-263987-ff6kor0c	290	129	a	a	DT
cord-263987-ff6kor0c	290	130	probabilistic	probabilistic	JJ
cord-263987-ff6kor0c	290	131	framework	framework	NN
cord-263987-ff6kor0c	290	132	for	for	IN
cord-263987-ff6kor0c	290	133	annotation	annotation	NN
cord-263987-ff6kor0c	290	134	of	of	IN
cord-263987-ff6kor0c	290	135	insertions	insertion	NNS
cord-263987-ff6kor0c	290	136	and	and	CC
cord-263987-ff6kor0c	290	137	deletions	deletion	NNS
cord-263987-ff6kor0c	290	138	in	in	IN
cord-263987-ff6kor0c	290	139	a	a	DT
cord-263987-ff6kor0c	290	140	multiple	multiple	JJ
cord-263987-ff6kor0c	290	141	alignment	alignment	NN
cord-263987-ff6kor0c	290	142	DNA	dna	NN
cord-263987-ff6kor0c	290	143	assembly	assembly	NN
cord-263987-ff6kor0c	290	144	with	with	IN
cord-263987-ff6kor0c	290	145	gaps	gap	NNS
cord-263987-ff6kor0c	290	146	(	(	-LRB-
cord-263987-ff6kor0c	290	147	Dawg	dawg	NN
cord-263987-ff6kor0c	290	148	)	)	-RRB-
cord-263987-ff6kor0c	290	149	:	:	:
cord-263987-ff6kor0c	290	150	simulating	simulate	VBG
cord-263987-ff6kor0c	290	151	sequence	sequence	NN
cord-263987-ff6kor0c	290	152	evolution	evolution	NN
cord-263987-ff6kor0c	290	153	INDELible	indelible	NN
cord-263987-ff6kor0c	290	154	:	:	:
cord-263987-ff6kor0c	290	155	a	a	DT
cord-263987-ff6kor0c	290	156	flexible	flexible	JJ
cord-263987-ff6kor0c	290	157	simulator	simulator	NN
cord-263987-ff6kor0c	290	158	of	of	IN
cord-263987-ff6kor0c	290	159	biological	biological	JJ
cord-263987-ff6kor0c	290	160	sequence	sequence	NN
cord-263987-ff6kor0c	290	161	evolution	evolution	NN
cord-263987-ff6kor0c	290	162	Biological	biological	JJ
cord-263987-ff6kor0c	290	163	sequence	sequence	NN
cord-263987-ff6kor0c	290	164	simulation	simulation	NN
cord-263987-ff6kor0c	290	165	for	for	IN
cord-263987-ff6kor0c	290	166	testing	test	VBG
cord-263987-ff6kor0c	290	167	complex	complex	JJ
cord-263987-ff6kor0c	290	168	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	290	169	hypotheses	hypothesis	NNS
cord-263987-ff6kor0c	290	170	:	:	:
cord-263987-ff6kor0c	290	171	indel	indel	NN
cord-263987-ff6kor0c	290	172	-	-	HYPH
cord-263987-ff6kor0c	290	173	Seq	Seq	NNP
cord-263987-ff6kor0c	290	174	-	-	HYPH
cord-263987-ff6kor0c	290	175	Gen	Gen	NNP
cord-263987-ff6kor0c	290	176	version	version	NN
cord-263987-ff6kor0c	290	177	2.0	2.0	CD
cord-263987-ff6kor0c	290	178	StatAlign	StatAlign	NNP
cord-263987-ff6kor0c	290	179	:	:	:
cord-263987-ff6kor0c	290	180	an	an	DT
cord-263987-ff6kor0c	290	181	extendable	extendable	JJ
cord-263987-ff6kor0c	290	182	software	software	NN
cord-263987-ff6kor0c	290	183	package	package	NN
cord-263987-ff6kor0c	290	184	for	for	IN
cord-263987-ff6kor0c	290	185	joint	joint	JJ
cord-263987-ff6kor0c	290	186	Bayesian	bayesian	JJ
cord-263987-ff6kor0c	290	187	estimation	estimation	NN
cord-263987-ff6kor0c	290	188	of	of	IN
cord-263987-ff6kor0c	290	189	alignments	alignment	NNS
cord-263987-ff6kor0c	290	190	and	and	CC
cord-263987-ff6kor0c	290	191	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	290	192	trees	tree	NNS
cord-263987-ff6kor0c	290	193	Advances	advance	VBZ
cord-263987-ff6kor0c	290	194	in	in	IN
cord-263987-ff6kor0c	290	195	Neural	Neural	NNP
cord-263987-ff6kor0c	290	196	Information	Information	NNP
cord-263987-ff6kor0c	290	197	Processing	Processing	NNP
cord-263987-ff6kor0c	290	198	Systems	Systems	NNPS
cord-263987-ff6kor0c	290	199	Erasing	erasing	NN
cord-263987-ff6kor0c	290	200	errors	error	NNS
cord-263987-ff6kor0c	290	201	due	due	JJ
cord-263987-ff6kor0c	290	202	to	to	IN
cord-263987-ff6kor0c	290	203	alignment	alignment	NN
cord-263987-ff6kor0c	290	204	ambiguity	ambiguity	NN
cord-263987-ff6kor0c	290	205	when	when	WRB
cord-263987-ff6kor0c	290	206	estimating	estimate	VBG
cord-263987-ff6kor0c	290	207	positive	positive	JJ
cord-263987-ff6kor0c	290	208	selection	selection	NN
cord-263987-ff6kor0c	290	209	StatAlign	StatAlign	NNP
cord-263987-ff6kor0c	290	210	2.0	2.0	CD
cord-263987-ff6kor0c	290	211	:	:	:
cord-263987-ff6kor0c	290	212	combining	combine	VBG
cord-263987-ff6kor0c	290	213	statistical	statistical	JJ
cord-263987-ff6kor0c	290	214	alignment	alignment	NN
cord-263987-ff6kor0c	290	215	with	with	IN
cord-263987-ff6kor0c	290	216	RNA	RNA	NNP
cord-263987-ff6kor0c	290	217	secondary	secondary	JJ
cord-263987-ff6kor0c	290	218	structure	structure	NN
cord-263987-ff6kor0c	290	219	prediction	prediction	NN
cord-263987-ff6kor0c	290	220	SimulFold	SimulFold	NNP
cord-263987-ff6kor0c	290	221	:	:	:
cord-263987-ff6kor0c	290	222	simultaneously	simultaneously	RB
cord-263987-ff6kor0c	290	223	inferring	infer	VBG
cord-263987-ff6kor0c	290	224	RNA	RNA	NNP
cord-263987-ff6kor0c	290	225	structures	structure	NNS
cord-263987-ff6kor0c	290	226	including	include	VBG
cord-263987-ff6kor0c	290	227	pseudoknots	pseudoknot	NNS
cord-263987-ff6kor0c	290	228	,	,	,
cord-263987-ff6kor0c	290	229	alignments	alignment	NNS
cord-263987-ff6kor0c	290	230	,	,	,
cord-263987-ff6kor0c	290	231	and	and	CC
cord-263987-ff6kor0c	290	232	trees	tree	NNS
cord-263987-ff6kor0c	290	233	using	use	VBG
cord-263987-ff6kor0c	290	234	a	a	DT
cord-263987-ff6kor0c	290	235	Bayesian	Bayesian	NNP
cord-263987-ff6kor0c	290	236	MCMC	MCMC	NNP
cord-263987-ff6kor0c	290	237	framework	framework	NN
cord-263987-ff6kor0c	290	238	Characterization	characterization	NN
cord-263987-ff6kor0c	290	239	of	of	IN
cord-263987-ff6kor0c	290	240	multiple	multiple	JJ
cord-263987-ff6kor0c	290	241	sequence	sequence	NN
cord-263987-ff6kor0c	290	242	alignment	alignment	NN
cord-263987-ff6kor0c	290	243	errors	error	NNS
cord-263987-ff6kor0c	290	244	using	use	VBG
cord-263987-ff6kor0c	290	245	complete	complete	JJ
cord-263987-ff6kor0c	290	246	-	-	HYPH
cord-263987-ff6kor0c	290	247	likelihood	likelihood	NN
cord-263987-ff6kor0c	290	248	score	score	NN
cord-263987-ff6kor0c	290	249	and	and	CC
cord-263987-ff6kor0c	290	250	position	position	NN
cord-263987-ff6kor0c	290	251	-	-	HYPH
cord-263987-ff6kor0c	290	252	shift	shift	NN
cord-263987-ff6kor0c	290	253	map	map	NN
cord-263987-ff6kor0c	290	254	Pacific	Pacific	NNP
cord-263987-ff6kor0c	290	255	Symposium	Symposium	NNP
cord-263987-ff6kor0c	290	256	on	on	IN
cord-263987-ff6kor0c	290	257	Biocomputing	Biocomputing	NNP
cord-263987-ff6kor0c	290	258	An	an	DT
cord-263987-ff6kor0c	290	259	efficient	efficient	JJ
cord-263987-ff6kor0c	290	260	algorithm	algorithm	NN
cord-263987-ff6kor0c	290	261	for	for	IN
cord-263987-ff6kor0c	290	262	statistical	statistical	JJ
cord-263987-ff6kor0c	290	263	multiple	multiple	JJ
cord-263987-ff6kor0c	290	264	alignment	alignment	NN
cord-263987-ff6kor0c	290	265	on	on	IN
cord-263987-ff6kor0c	290	266	arbitrary	arbitrary	JJ
cord-263987-ff6kor0c	290	267	phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	290	268	trees	tree	NNS
cord-263987-ff6kor0c	290	269	Weighted	weight	VBN
cord-263987-ff6kor0c	290	270	finite	finite	JJ
cord-263987-ff6kor0c	290	271	-	-	HYPH
cord-263987-ff6kor0c	290	272	state	state	NN
cord-263987-ff6kor0c	290	273	transducers	transducer	NNS
cord-263987-ff6kor0c	290	274	in	in	IN
cord-263987-ff6kor0c	290	275	speech	speech	NN
cord-263987-ff6kor0c	290	276	recognition	recognition	NN
cord-263987-ff6kor0c	290	277	Automata	automata	NN
cord-263987-ff6kor0c	290	278	-	-	HYPH
cord-263987-ff6kor0c	290	279	theoretic	theoretic	JJ
cord-263987-ff6kor0c	290	280	models	model	NNS
cord-263987-ff6kor0c	290	281	of	of	IN
cord-263987-ff6kor0c	290	282	mutation	mutation	NN
cord-263987-ff6kor0c	290	283	and	and	CC
cord-263987-ff6kor0c	290	284	alignment	alignment	NN
cord-263987-ff6kor0c	290	285	Historian	historian	NN
cord-263987-ff6kor0c	290	286	:	:	:
cord-263987-ff6kor0c	290	287	accurate	accurate	JJ
cord-263987-ff6kor0c	290	288	reconstruction	reconstruction	NN
cord-263987-ff6kor0c	290	289	of	of	IN
cord-263987-ff6kor0c	290	290	ancestral	ancestral	JJ
cord-263987-ff6kor0c	290	291	sequences	sequence	NNS
cord-263987-ff6kor0c	290	292	and	and	CC
cord-263987-ff6kor0c	290	293	evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	290	294	rates	rate	NNS
cord-263987-ff6kor0c	291	1	Phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	291	2	quantification	quantification	NN
cord-263987-ff6kor0c	291	3	of	of	IN
cord-263987-ff6kor0c	291	4	intra	intra	JJ
cord-263987-ff6kor0c	291	5	-	-	JJ
cord-263987-ff6kor0c	291	6	tumour	tumour	JJ
cord-263987-ff6kor0c	291	7	heterogeneity	heterogeneity	NN
cord-263987-ff6kor0c	291	8	Protein	Protein	NNP
cord-263987-ff6kor0c	291	9	family	family	NN
cord-263987-ff6kor0c	291	10	classification	classification	NN
cord-263987-ff6kor0c	291	11	using	use	VBG
cord-263987-ff6kor0c	291	12	sparse	sparse	JJ
cord-263987-ff6kor0c	291	13	Markov	Markov	NNP
cord-263987-ff6kor0c	291	14	transducers	transducer	NNS
cord-263987-ff6kor0c	292	1	Modular	modular	JJ
cord-263987-ff6kor0c	292	2	non	non	JJ
cord-263987-ff6kor0c	292	3	-	-	JJ
cord-263987-ff6kor0c	292	4	repeating	repeating	JJ
cord-263987-ff6kor0c	292	5	codes	code	NNS
cord-263987-ff6kor0c	292	6	for	for	IN
cord-263987-ff6kor0c	292	7	DNA	dna	NN
cord-263987-ff6kor0c	292	8	storage	storage	NN
cord-263987-ff6kor0c	292	9	A	a	DT
cord-263987-ff6kor0c	292	10	method	method	NN
cord-263987-ff6kor0c	292	11	for	for	IN
cord-263987-ff6kor0c	292	12	synthesizing	synthesize	VBG
cord-263987-ff6kor0c	292	13	sequential	sequential	JJ
cord-263987-ff6kor0c	292	14	circuits	circuit	NNS
cord-263987-ff6kor0c	292	15	Simultaneous	simultaneous	JJ
cord-263987-ff6kor0c	292	16	solution	solution	NN
cord-263987-ff6kor0c	292	17	of	of	IN
cord-263987-ff6kor0c	292	18	the	the	DT
cord-263987-ff6kor0c	292	19	RNA	RNA	NNP
cord-263987-ff6kor0c	292	20	folding	folding	NN
cord-263987-ff6kor0c	292	21	,	,	,
cord-263987-ff6kor0c	292	22	alignment	alignment	NN
cord-263987-ff6kor0c	292	23	,	,	,
cord-263987-ff6kor0c	292	24	and	and	CC
cord-263987-ff6kor0c	292	25	protosequence	protosequence	NN
cord-263987-ff6kor0c	292	26	problems	problem	NNS
cord-263987-ff6kor0c	292	27	Evolutionary	evolutionary	JJ
cord-263987-ff6kor0c	292	28	triplet	triplet	NN
cord-263987-ff6kor0c	292	29	models	model	NNS
cord-263987-ff6kor0c	292	30	of	of	IN
cord-263987-ff6kor0c	292	31	structured	structured	JJ
cord-263987-ff6kor0c	292	32	RNA	RNA	NNP
cord-263987-ff6kor0c	292	33	MCALIGN2	mcalign2	NN
cord-263987-ff6kor0c	292	34	:	:	:
cord-263987-ff6kor0c	293	1	faster	fast	RBR
cord-263987-ff6kor0c	293	2	,	,	,
cord-263987-ff6kor0c	293	3	accurate	accurate	JJ
cord-263987-ff6kor0c	293	4	global	global	JJ
cord-263987-ff6kor0c	293	5	pairwise	pairwise	JJ
cord-263987-ff6kor0c	293	6	alignment	alignment	NN
cord-263987-ff6kor0c	293	7	of	of	IN
cord-263987-ff6kor0c	293	8	non	non	JJ
cord-263987-ff6kor0c	293	9	-	-	JJ
cord-263987-ff6kor0c	293	10	coding	coding	JJ
cord-263987-ff6kor0c	293	11	DNA	dna	NN
cord-263987-ff6kor0c	293	12	sequences	sequence	NNS
cord-263987-ff6kor0c	293	13	based	base	VBN
cord-263987-ff6kor0c	293	14	on	on	IN
cord-263987-ff6kor0c	293	15	explicit	explicit	JJ
cord-263987-ff6kor0c	293	16	models	model	NNS
cord-263987-ff6kor0c	293	17	of	of	IN
cord-263987-ff6kor0c	293	18	indel	indel	NN
cord-263987-ff6kor0c	293	19	evolution	evolution	NN
cord-263987-ff6kor0c	294	1	A	a	DT
cord-263987-ff6kor0c	294	2	hidden	hidden	JJ
cord-263987-ff6kor0c	294	3	Markov	Markov	NNP
cord-263987-ff6kor0c	294	4	model	model	NN
cord-263987-ff6kor0c	294	5	approach	approach	NN
cord-263987-ff6kor0c	294	6	to	to	IN
cord-263987-ff6kor0c	294	7	variation	variation	NN
cord-263987-ff6kor0c	294	8	among	among	IN
cord-263987-ff6kor0c	294	9	sites	site	NNS
cord-263987-ff6kor0c	294	10	in	in	IN
cord-263987-ff6kor0c	294	11	rate	rate	NN
cord-263987-ff6kor0c	294	12	of	of	IN
cord-263987-ff6kor0c	294	13	evolution	evolution	NN
cord-263987-ff6kor0c	294	14	Phylogenetic	phylogenetic	JJ
cord-263987-ff6kor0c	294	15	estimation	estimation	NN
cord-263987-ff6kor0c	294	16	of	of	IN
cord-263987-ff6kor0c	294	17	context	context	NN
cord-263987-ff6kor0c	294	18	-	-	HYPH
cord-263987-ff6kor0c	294	19	dependent	dependent	JJ
cord-263987-ff6kor0c	294	20	substitution	substitution	NN
cord-263987-ff6kor0c	294	21	rates	rate	NNS
cord-263987-ff6kor0c	294	22	by	by	IN
cord-263987-ff6kor0c	294	23	maximum	maximum	JJ
cord-263987-ff6kor0c	294	24	likelihood	likelihood	NN
cord-263987-ff6kor0c	294	25	RNA	RNA	NNP
cord-263987-ff6kor0c	294	26	secondary	secondary	JJ
cord-263987-ff6kor0c	294	27	structure	structure	NN
cord-263987-ff6kor0c	294	28	prediction	prediction	NN
cord-263987-ff6kor0c	294	29	using	use	VBG
cord-263987-ff6kor0c	294	30	stochastic	stochastic	JJ
cord-263987-ff6kor0c	294	31	context	context	NN
cord-263987-ff6kor0c	294	32	-	-	HYPH
cord-263987-ff6kor0c	294	33	free	free	JJ
cord-263987-ff6kor0c	294	34	grammars	grammar	NNS
cord-263987-ff6kor0c	295	1	XRate	XRate	NNP
cord-263987-ff6kor0c	295	2	:	:	:
cord-263987-ff6kor0c	295	3	a	a	DT
cord-263987-ff6kor0c	295	4	fast	fast	JJ
cord-263987-ff6kor0c	295	5	prototyping	prototyping	NN
cord-263987-ff6kor0c	295	6	,	,	,
cord-263987-ff6kor0c	295	7	training	training	NN
cord-263987-ff6kor0c	295	8	and	and	CC
cord-263987-ff6kor0c	295	9	annotation	annotation	NN
cord-263987-ff6kor0c	295	10	tool	tool	NN
cord-263987-ff6kor0c	295	11	for	for	IN
cord-263987-ff6kor0c	295	12	phylo	phylo	NN
cord-263987-ff6kor0c	295	13	-	-	HYPH
cord-263987-ff6kor0c	295	14	grammars	grammar	NNS
cord-263987-ff6kor0c	296	1	The	the	DT
cord-263987-ff6kor0c	296	2	author	author	NN
cord-263987-ff6kor0c	296	3	thanks	thank	NNS
cord-263987-ff6kor0c	296	4	Kiyoshi	Kiyoshi	NNP
cord-263987-ff6kor0c	296	5	Ezawa	Ezawa	NNP
cord-263987-ff6kor0c	296	6	,	,	,
cord-263987-ff6kor0c	296	7	Elena	Elena	NNP
cord-263987-ff6kor0c	296	8	Rivas	Rivas	NNP
cord-263987-ff6kor0c	296	9	,	,	,
cord-263987-ff6kor0c	296	10	Sean	Sean	NNP
cord-263987-ff6kor0c	296	11	Eddy	Eddy	NNP
cord-263987-ff6kor0c	296	12	,	,	,
cord-263987-ff6kor0c	296	13	Jeff	Jeff	NNP
cord-263987-ff6kor0c	296	14	Thorne	Thorne	NNP
cord-263987-ff6kor0c	296	15	,	,	,
cord-263987-ff6kor0c	296	16	Benjamin	Benjamin	NNP
cord-263987-ff6kor0c	296	17	Redelings	Redelings	NNP
cord-263987-ff6kor0c	296	18	,	,	,
cord-263987-ff6kor0c	296	19	Marc	Marc	NNP
cord-263987-ff6kor0c	296	20	Suchard	Suchard	NNP
cord-263987-ff6kor0c	296	21	,	,	,
cord-263987-ff6kor0c	296	22	and	and	CC
cord-263987-ff6kor0c	296	23	one	one	CD
cord-263987-ff6kor0c	296	24	anonymous	anonymous	JJ
cord-263987-ff6kor0c	296	25	referee	referee	NN
cord-263987-ff6kor0c	296	26	for	for	IN
cord-263987-ff6kor0c	296	27	productive	productive	JJ
cord-263987-ff6kor0c	296	28	conversations	conversation	NNS
cord-263987-ff6kor0c	296	29	that	that	WDT
cord-263987-ff6kor0c	296	30	have	have	VBP
cord-263987-ff6kor0c	296	31	informed	inform	VBN
cord-263987-ff6kor0c	296	32	this	this	DT
cord-263987-ff6kor0c	296	33	review	review	NN
cord-263987-ff6kor0c	296	34	.	.	.
cord-263987-ff6kor0c	297	1	This	this	DT
cord-263987-ff6kor0c	297	2	work	work	NN
cord-263987-ff6kor0c	297	3	was	be	VBD
cord-263987-ff6kor0c	297	4	supported	support	VBN
cord-263987-ff6kor0c	297	5	by	by	IN
cord-263987-ff6kor0c	297	6	NIH	NIH	NNP
cord-263987-ff6kor0c	297	7	/	/	SYM
cord-263987-ff6kor0c	297	8	NHGRI	NHGRI	NNP
cord-263987-ff6kor0c	297	9	grant	grant	VBP
cord-263987-ff6kor0c	297	10	HG004483	hg004483	NN
cord-263987-ff6kor0c	297	11	.	.	.
cord-263987-ff6kor0c	298	1	Authors	author	NNS
cord-263987-ff6kor0c	298	2	'	'	POS
cord-263987-ff6kor0c	298	3	contributions	contribution	NNS
cord-263987-ff6kor0c	298	4	IH	IH	NNP
cord-263987-ff6kor0c	298	5	wrote	write	VBD
cord-263987-ff6kor0c	298	6	the	the	DT
cord-263987-ff6kor0c	298	7	article	article	NN
cord-263987-ff6kor0c	298	8	.	.	.
cord-263987-ff6kor0c	299	1	The	the	DT
cord-263987-ff6kor0c	299	2	author	author	NN
cord-263987-ff6kor0c	299	3	declares	declare	VBZ
cord-263987-ff6kor0c	299	4	that	that	IN
cord-263987-ff6kor0c	299	5	they	-PRON-	PRP
cord-263987-ff6kor0c	299	6	have	have	VBP
cord-263987-ff6kor0c	299	7	no	no	DT
cord-263987-ff6kor0c	299	8	competing	compete	VBG
cord-263987-ff6kor0c	299	9	interests	interest	NNS
cord-263987-ff6kor0c	299	10	.	.	.
cord-263987-ff6kor0c	300	1	Not	not	RB
cord-263987-ff6kor0c	300	2	applicable	applicable	JJ
cord-263987-ff6kor0c	300	3	.	.	.
cord-263987-ff6kor0c	301	1	Not	not	RB
cord-263987-ff6kor0c	301	2	applicable	applicable	JJ
cord-263987-ff6kor0c	301	3	.	.	.
cord-263987-ff6kor0c	302	1	Springer	Springer	NNP
cord-263987-ff6kor0c	302	2	Nature	Nature	NNP
cord-263987-ff6kor0c	302	3	remains	remain	VBZ
cord-263987-ff6kor0c	302	4	neutral	neutral	JJ
cord-263987-ff6kor0c	302	5	with	with	IN
cord-263987-ff6kor0c	302	6	regard	regard	NN
cord-263987-ff6kor0c	302	7	to	to	IN
cord-263987-ff6kor0c	302	8	jurisdictional	jurisdictional	JJ
cord-263987-ff6kor0c	302	9	claims	claim	NNS
cord-263987-ff6kor0c	302	10	in	in	IN
cord-263987-ff6kor0c	302	11	published	publish	VBN
cord-263987-ff6kor0c	302	12	maps	map	NNS
cord-263987-ff6kor0c	302	13	and	and	CC
cord-263987-ff6kor0c	302	14	institutional	institutional	JJ
cord-263987-ff6kor0c	302	15	affiliations	affiliation	NNS
cord-263987-ff6kor0c	302	16	.	.	.
cord-263987-ff6kor0c	303	1	Received	receive	VBN
cord-263987-ff6kor0c	303	2	:	:	:
cord-263987-ff6kor0c	303	3	9	9	CD
cord-263987-ff6kor0c	303	4	January	January	NNP
cord-263987-ff6kor0c	303	5	2017	2017	CD
cord-263987-ff6kor0c	304	1	Accepted	accept	VBN
cord-263987-ff6kor0c	304	2	:	:	:
cord-263987-ff6kor0c	304	3	30	30	CD
cord-263987-ff6kor0c	304	4	April	April	NNP
cord-263987-ff6kor0c	304	5	2017	2017	CD