id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-313247-55loucvc	Pipes, Lenore	Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny	2020-10-07		.txt	text/plain	2546	209	64	We investigate several different strategies for rooting the SARS-CoV-2 tree and provide measures of statistical uncertainty for all methods. Our results suggest that inferences on the origin and early spread of SARS-CoV-2 based on rooted trees should be interpreted with caution. There are many different methods for inferring the root of a phylogenetic tree, but they largely depend on three possible sources of information: outgroups, the molecular clock, and non-reversibility. To investigate the possible rootings of the SARS-CoV-2 phylogeny we used six different methods and quantified the uncertainty in the placement of the root for each method on the inferred maximum likelihood topology. We note that while interpretation of bootstrap proportions in phylogenetics can be problematic (see Efron et al., 1996) we performed 1,000 parametric simulations using pyvolve (Spielman and Wilke, 2015) using maximum likelihood estimates, from the original data set, of the model of molecular evolution and the phylogenetic tree, including branch lengths (see Table S2 ).	./cache/cord-313247-55loucvc.txt	./txt/cord-313247-55loucvc.txt