Software Development
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. Current version: v1.10.1

BEAST, Bayesian Evolutionary Analysis Sampling Trees, is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. The program is orientated towards (strict and relaxed) molecular clock analyses...

Produce high-quality figures of phylogenetic trees Current version: v1.4.4

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...

A manual sequence alignment editor. Current version: v2.0a11

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: v1.3.4

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...

Explore temporal signal and clocklikeness in trees (formerly Path-O-Gen) Current version: v1.5.3

TempEst 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 program for analysing results from Bayesian MCMC programs such as BEAST & MrBayes Current version: v1.7.1

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...

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This may mean they no longer run on newer computers or the analyses have been superceded by other software
Explore temporal signal and clocklikeness in trees
Description: Path-O-Gen has been renamed TempEst. Please click here to be redirected to the TempEst page...
Andrew Rambaut, 2007