We describe a novel model and algorithm for simultaneously estimating multiple molecular
sequence alignments and the phylogenetic trees that relate the sequences. Unlike current …

BAli-Phy is a Bayesian posterior sampler that employs Markov chain Monte Carlo to explore
the joint space of alignment and phylogeny given molecular sequence data. Simultaneous …

Currently available phylogenetic methods for studying the rate of evolution in a continuously
valued character assume that the rate is constant throughout the tree or that it changes …

… We introduce a new indel model to remedy a shortcoming of the Redelings and Suchard (…
We further enhance the estimation method of Redelings and Suchard [24] by introducing a …

Recent years have witnessed a proliferation of quantitative methods for biogeographic inference.
In particular, novel parametric approaches represent exciting new opportunities for the …

We present a new supertree method that enables rapid estimation of a summary tree on the
scale of millions of leaves. This supertree method summarizes a collection of input …

The Caloplaca saxicola group is the main group of saxicolous, lobed-effigurate species within
genus Caloplaca (Teloschistaceae, lichen-forming Ascomycota). A recent monographic …

To evaluate the current delimitation of broadly distributed morphospecies from the Lecanora
dispersa group, the nuclear ribosomal internal transcribed spacer region (ITS1, 5.8S and …

We describe improvements to BAli-Phy, a Markov chain Monte Carlo (MCMC) program that
jointly estimates phylogeny, alignment and other parameters from unaligned sequence data. …

To assess the conventional treatment in evolutionary inference of alignment gaps as missing
data, we propose a simple nonparametric test of the null hypothesis that the locations of …