Phylogenetics software development
Applications of phylogenetics are completely reliant on having software available.
Two leading software phylogenetics packages, the BEAST family of software and PhyML, were authored by members of the group and continue to be developed here. These packages have user bases in the thousands, PhyML has been cited over 12,500 times while the BEAST software (and supporting methodological papers) have been cited >17,200 times (Google scholar).
Members of the group are involved in running training courses on how to best use the software and different methodologies. Check events page and sign up to the mailing list to be informed when courses are scheduled.
BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user interface for setting up standard analyses and a suite of programs for analysing the results.
DensiTree is a program for qualitative analysis of sets of trees that make it possible to visually inspect the posterior distribution of an MCMC run over a tree. Many features of the posterior distribution are easily visible, such as agreement/disagreement of tree topologies, uncertainty in node heights and relative dominance of particular topologies.
Tracer is a software package for visualising and analysing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more. It can read output files from MrBayes, BEAST, BEAST2, RevBayes, Migrate, LAMARC and possibly other MCMC programs from other domains.
BioGeoBEARS is an R package, authored by Nicholas J. Matzke, that is designed to perform inference of biogeographic history on phylogenies, and also model testing and model choice of the many different possible models of how biogeography may evolve on a phylogeny (dispersal, vicariance, founder-event speciation, DEC, DIVA, BAYAREA, etc.)
Geneious is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc.