id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-321715-bkfkmtld	Redelings, Benjamin D	Incorporating indel information into phylogeny estimation for rapidly emerging pathogens	2007-03-14		.txt	text/plain	9793	546	54	To see if indel information improves phylogenetic resolution we compare the number of bi-partitions that are supported under the joint model and the traditional sequential approach, in which topology reconstruction assumes a previously determined alignment. These parameters include a multiple alignment A that specifies the positional homology between the sequences Y, an evolutionary tree (τ, T) where τ is an unrooted bifurcating tree topology and T = (t 1 , ..., t 2N -3 ) is a vector of branch lengths along the edges in τ, and vectors Θ and Λ are parameters that characterize the letter substitution and indel processes respectively. We therefore propose a new pairwise alignment prior that maintains a fixed sequence length distribution φ even when the indel probability varies from branch to branch. Since the joint model balances substitution and indel information as well as taking alignment ambiguity into account we assume that these differences represent an improvement in the accuracy of estimation.	./cache/cord-321715-bkfkmtld.txt	./txt/cord-321715-bkfkmtld.txt