The field of phylogenetics is entering a new era in which trees of historical relationships
between species are increasingly inferred from multilocus and genomic data. A major …

Bayesian methods have become very popular in molecular phylogenetics due to the
availability of user-friendly software for running sophisticated models of evolution. However …

Motivation: Increasing attention has been devoted to estimation of species-level
phylogenetic relationships under the coalescent model. However, existing methods either …

This paper provides an overview and a tutorial of the BPP program, which is a Bayesian
MCMC program for analyzing multi-locus genomic sequence data under the multispecies …

Since its introduction in 2001, MrBayes has grown in popularity as a software package for
Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With …

Until recently, it has been common practice for a phylogenetic analysis to use a single gene
sequence from a single individual organism as a proxy for an entire species. With …

The multispecies coalescent has provided important progress for evolutionary inferences,
including increasing the statistical rigor and objectivity of comparisons among competing …

The multispecies coalescent provides an elegant theoretical framework for estimating
species trees and species demographics from genetic markers. However, practical …

Background Several phylogenetic approaches have been developed to estimate species
trees from collections of gene trees. However, maximum likelihood approaches for …

The advent and maturation of algorithms for estimating species trees—phylogenetic trees
that allow gene tree heterogeneity and whose tips represent lineages, populations and …