Description:

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards molecular clock analyses. It is intended not only as a method of constructing phylogenies but also of testing evolutionary hypotheses sampled over probable tree-space...

Description:

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program...

Description: Path-O-Gen is a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. It can read and analyse contemporaneous trees (where all sequences have been collected at the same time) and dated-tip trees (where sequences have been collected at different dates)...

Description:

WARNING: Se-Al will not run on Mac OS X 10.7

Due to the lack of support for older PPC code (via the 'Rosetta' system present in older versions)...

Description: Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process...

Description:

Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs.

Although Tracer can be used with programs other than BEAST, users are strongly advised to join the BEAST mailing-list...

Description: TreeStat is an application that can process a set of trees in a PHYLIP or NEXUS format tree file and calculate a number of summary statistics for each...

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