Abstract paml, currently in version 4, is a package of programs for phylogenetic analyses of
DNA and protein sequences using maximum likelihood (ML). The programs may be used to …

▪ Abstract The continuous flow of genomic data is creating unprecedented opportunities for
the reconstruction of molecular phylogenies. Access to whole-genome data means that …

Abstract The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package
has become a primary tool for Bayesian phylogenetic and phylodynamic inference from …

Historical biogeography has a diversity of methods for inferring ancestral geographic ranges
on phylogenies, but many of the methods have conflicting assumptions, and there is no …

Computational evolutionary biology, statistical phylogenetics and coalescent-based
population genetics are becoming increasingly central to the analysis and understanding of …

There are two competing hypotheses for the origin of the Indo-European language family.
The conventional view places the homeland in the Pontic steppes about 6000 years ago. An …

Abstract Model selection is a topic of special relevance in molecular phylogenetics that
affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental …

Research aimed at understanding the geographic context of evolutionary histories is
burgeoning across biological disciplines. Recent endeavors attempt to interpret …

The field of molecular evolution has experienced explosive growth in recent years due to the
rapid accumulation of genetic sequence data, continuous improvements to computer …

In the Bayesian paradigm, a common method for comparing two models is to compute the
Bayes factor, defined as the ratio of their respective marginal likelihoods. In recent …