For analysis of phlyogenies. Includes a wide range of randomisation methods, consensus methods, tree comparison measures, and calculates reconciled trees. Now aging, and available only for Windows machines, but still has some unique features. Much of the taxonomy.zoology.gla.ac.uk/rod/cpw.html
Joe Felsenstein's suite of programs implementing perhaps the widest range of phylogenetic inference package. The most widely distributed phylogeny software. Includes distance, likelihood and parsimony methods for a wide range of different types of data, a evolution.genetics.washington.edu/phylip.html
Java application for drawing phylogenetic trees. Allows you to save in various formats, print, edit, modify, and adorn the tree, and should work on any java runtime platform. iubio.bio.indiana.edu/soft/molbio/java/apps/trees
A powerful Macintosh package for phylogenetic analysis. Not intended as a stand-alone tool to infer phylogeny, but excels in studying character evolution. Also provides tools for entering and editing data and phylogenies and producing attractive tree diag phylogeny.arizona.edu/macclade/macclade.html
Uses reconciled trees to compare gene trees and species trees, explaining incongruence between the phylogenies by postulating horizontal transfer, gene duplication and loss events. Reprints of papers describing the methods are available from the GeneTree taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html
Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them. pbil.univ-lyon1.fr/software/phylowin.html
Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms. mesquiteproject.org/mesquite/mesquite.html
PAUP is the most widely used package for phylogenetic inference, and now implements maximum likelihood and distance methods as well as various forms of parsimony. Powerful and very easy to use, particularly the Mac version. paup.csit.fsu.edu
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