Luckly, the information age has made inferring phylogenies easier than ever. Many software packages now exist to help weakling biologists figure out their complex datasets. Unfortunately, many of these otherwise great packages are Windows only! Since I have to do phylogenetic analyses on DNA sequence data all the time, and all I have is a paltry MacBook, I’ve had to find some alternatives. Here they are:
Don’t let the Windows 3.11-themed website fool you, PHYLIP is a great program! In the absence of MEGA 4 , its absolutely your best best for most phylogenetic analysis. Its capable of most basic tree building methods (parsimony, neighbor-joining, maximum likelyhood) and can generate DNA sequence statistics. Plus, its open-source!
If you’re going to use PHYLIP, you’ll need to find the appropriate model of nucleotide substitution for your sequences. ModelGenerator is a nice little Java application that figures it out for you! Ace!
BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a brand new, easy-to-use package of programs for conducting Bayesian Markov Chain Monte Carlo analysis on phylogenetic data. I recently used it for a school project, and I was blown away with how well-designed and powerful it was. Besides MEGA 4, it is probably the most user-friendly phylogenetics program I’ve ever used. Amazing!
One big problem with Windows phylogenetics programs is that they generate Windows-looking trees. Nobody wants to see that, and Mac users can use FigTree (from the makers of BEAST) to generate deliciously anti-aliased, high resolution phylogenies. Mondo!
Both of these programs are commerical phylogenetics programs for Mac OS X. They are super-feature rich and are cited all the time in evolution papers. Although you can pull off most analyses with free programs, if you have your own lab with a fat grant, these programs are likely the way to go.