An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree.

ABSTRACT:

Motivation

Gene tree represents the evolutionary history of gene lineages that originate from multiple related populations. Under the multispecies coalescent model, lineages may coalesce outside the species (population) boundary. Given a species tree (with branch lengths), the gene tree probability is the probability of observing a specific gene tree topology under the multispecies coalescent model. There are two existing algorithms for computing the exact gene tree probability. The first algorithm is due to Degnan and Salter, where they enumerate all the so-called coalescent histories for the given species tree and the gene tree topology. Their algorithm runs in exponential time in the number of gene lineages in general. The second algorithm is the STELLS algorithm (2012), which i

SUBMITTER: Wu Y 

PROVIDER: S-EPMC4908345 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature