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MrBayes

MrBayes is a program for the Bayesian estimation of phylogeny and evolution. The current version is written by John Huelsenbeck (University of California, San Diego) and Fredrik Ronquist (Florida State University) but the next major release will be co-authored by Paul van der Mark (Florida State University), Bret Larget (University of Wisconsin, Madison), and Donald Simon (Duquesne University). MrBayes handles a wide variety of stochastic evolutionary models for molecular, morphological and other types of discrete data. It uses Metropolis-coupled Markov chain Monte Carlo techniques to estimate the posterior probability distribution. The program has a command-line interface and runs on all common platforms, including MPI-enabled cluster computers and shared-memory machines. The source code and executables are distributed free of charge from http://www.mrbayes.net.

TreeFitter

Written by Fredrik Ronquist, TreeFitter is a program for parsimony-based tree fitting. This is a technique that finds applications in gene tree - species tree fitting as well as in coevolutionary and biogeographic studies. TreeFitter has a command-line interface and implements some of the fastest algorithms known for parsimony-based tree fitting with horizontal transfer / host switches / dispersal events allowed. The user can fit single trees to each other, or reconstruct species trees / host trees / general area cladograms from large sets of gene trees / parasite trees / organism phylogenies. TreeFitter is provided as executables for Macintosh and Windows machines at http://www.ebc.uu.se/systzoo/research/treefitter/treefitter.html.

DIVA

This program, authored by Fredrik Ronquist, implements a parsimony technique for reconstructing ancestral distributions of organisms known as Dispersal-Vicariance Analysis. The program has a command-line interface and is provided as executables for Macintosh and Windows machines at http://www.ebc.uu.se/systzoo/research/diva/diva.html.

Character matrices

To come