id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-297530-7zbvgvk8	Kühnert, Denise	Phylogenetic and epidemic modeling of rapidly evolving infectious diseases	2011-08-31		.txt	text/plain	12826	629	42	By using Kingman's coalescent as a prior density on trees, Bayesian inference can be used to simultaneously estimate the phylogeny of the viral sequences and the demographic history of the virus population (Drummond et al., 2002 (Drummond et al., , 2005 , see Box 1). A maximum likelihood based method (the single rate dated tips (SRDT) model; Rambaut, 2000) , estimates ancestral divergence times and overall substitution rate on a fixed tree, assuming a strict molecular clock. While the generalized skyline plot is a good tool for data exploration, and to assist in model selection (e.g., Pybus et al., 2003; Lemey et al., 2004) , it infers demographic history based on a single input tree and therefore does not account for sampling error produced by phylogenetic reconstruction nor for the intrinsic stochasticity of the coalescent process.	./cache/cord-297530-7zbvgvk8.txt	./txt/cord-297530-7zbvgvk8.txt