What is the best free software for phylogeny analysis?

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Sarah Wells

Unfortunately, Geneious is by far the best sequence alignment software, but yes it is expensive. Ask around at your institution to see if someone already has a license that you can share.

For tree building, it depends what type of analysis you want to do, but the majority of the most popular programs are free. MEGA (http://www.megasoftware.net/) is useful for initial data exploration and for constructing quick and dirty Neighbour-Joining trees. GARLI (http://www.bio.utexas.edu/faculty/antisense/garli/Garli.html) is a great free software for maximum likelihood (ML) phylogenetic reconstruction with some great online tutorials (e.g. http://evomics.org/learning/phylogenetics/garli/). PAUP* (http://paup.csit.fsu.edu/) also uses ML, and it has a plugin for Geneious anyway.

BEAST (http://beast.bio.ed.ac.uk/) is probably the most extensive software for Bayesian analysis and has a lot of online documentation. As well as phylogenetic reconstruction, you can also use it to test evolutionary hypotheses about your data.