A Question About Phylogenetics Software

There are a number of papers with datasets in the paleoanthropological literature that I am wanting to play around with but I can’t afford PAUP. So I am throwing the question to my readers…Other than PAUP are there any good phylogenetic programs out there? Programs that can be used for continuous and discrete characters? Preferably free?

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5 Responses

  1. It’s all about PHYLIP.
    The phylogenetics package that started it all, created by the world’s leading expert in phylogenetics (and professor in my department), Joe Felsenstein. And it’s 100% free!

    website: http://evolution.genetics.washington.edu/phylip.html

    you might also want to check out his extremely comprehensive list of every phylo program in existence:

    http://evolution.gs.washington.edu/phylip/software.html

    hope this helps!

  2. Thanks! I will look into both of them.

  3. I used to use Hennig86 on DOS, which it turns out you can still get. But I second the suggestion for Mesquite; it’s probably the best for trait data. If you get into molecular data, there are a lot of other options, including some web-based systems.

  4. At this point I am just looking at trait data..

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