title: Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts.
abstract: The field of phylogenetic tree estimation has been dominated by three broad classes of methods: distance-based approaches, parsimony and likelihood-based methods (including maximum likelihood (ML) and Bayesian approaches). Here we introduce two new approaches to tree inference: pairwise likelihood estimation and a distance-based method that estimates the number of substitutions along the paths through the tree. Our results include the derivation of the formulae for the probability that two leaves will be identical at a site given a number of substitutions along the path connecting them. We also derive the posterior probability of the number of substitutions along a path between two sequences. The calculations for the posterior probabilities are exact for group-based, symmetric models of character evolution, but are only approximate for more general models.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States. mtholder@ku.edu
authors.forename: Mark T
authors.initials: MT
authors.lastname: Holder
authors.forename: Mike
authors.initials: M
authors.lastname: Steel
mesh_terms: D019143:Evolution, Molecular; D008957:Models, Genetic; D010802:Phylogeny