Software Development
BEAST can be obtained from: http://mcmc.googlecode.com
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...

Produce high-quality figures of phylogenetic trees Current version: v1.4
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...

Explore temporal signal and clocklikeness in trees Current version: v1.4
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)...
A manual sequence alignment editor. Current version: v2.0a11
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)...

An application for the Monte Carlo simulation of DNA and amino acid sequence evolution along phyloge(...) Current version: v1.3.3
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...
A program for analysing results from Bayesian MCMC programs such as BEAST & MrBayes Current version: v1.6
Description:

by Andrew Rambaut, Marc Suchard & Alexei Drummond

Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain)...

A program that calculates summary statistics of a set of trees Current version: v1.2
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...

The following programs are now no longer supported
This may mean they no longer run on newer computers or the analyses have been superceded by other software
 
Andrew Rambaut, 2007