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. 

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BEAST 2

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 suit of programs for analysing the results.

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DensiTree

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.

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PhyML

PhyML is a fast maximum likelihood phylogeny estimator from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. PhyML is open source distributed under the terms of the GNU GPL.

 

 

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PhyTime

PhyTime is a software that estimates divergence times from the analysis of DNA or protein sequences. It relies on a fast Bayesian approach that builds the posterior densities of node ages. The method and its performances are described in Guindon, 2010, Mol. Biol. Evol. Please click here to download it.

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Fitmodel

Fitmodel estimates the parameters of various codon-based models of substitution, including those described in Guindon, Rodrigo, Dyer and Huelsenbeck, 2004, PNAS. These models are especially useful as they accommodate site-specific switches between selection regimes without a priori knowledge of the positions in the tree where changes of selection regimes occurred. Click here to download.

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Geneious

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.

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PAL - Phylogenetics Analysis Library

The PAL project is a collaborative effort to provide a high quality open source Java library for use in molecular evolution and phylogenetics.

 

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Java Evolutionary Biology Library

An open source Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees. The source code is hosted at http://sourceforge.net/projects/jebl