TreeMap
Experimental program for comparing host and parasite trees.

TreeView
Simple program for displaying phylogenies.

Component
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 functionality is now replaced by RadCon, GeneTree, TreeMap and the latest release of PAUP.

PHYLIP
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, and runs on most platforms.

Phylodendron
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.

MacClade
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 diagrams and charts.

RadCon
A package implementing a wide range of consensus methods, including reduced consensus, and for calculation of MRP supertrees. Currently only available for Macs.

GeneTree
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 web page. Available for Macintosh and Windows.

Tree Puzzle
Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.

Nona - A Quick Guide to the Commands
A brief overview of using Nona for phylogenetic analysis.

SuperTree
Implements various supertree building methods. Available in Linux/Unix and PC versions.

Phylo-Win
Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.

PAML
Phylogenetic analyses of DNA or protein sequences using maximum likelihood.

MrBayes
Bayesian inference of phylogeny using Markov Chain Monte Carlo methods.

Mesquite
Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms.

PAUP*
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.