Software

Clann: Software for Supertree Methods
Clann implements a large number of supertree methods for reconstructing phylogenies from sets of input phylogenetic trees.
http://bioinf.may.ie/software/clann/

Component
For analysis of phylogenies. Includes a wide range of randomization 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.
http://taxonomy.zoology.gla.ac.uk/rod/cpw.html

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.
http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html

3I - Internet-accessible Interactive Identification
Program to create internet-accessible interactive taxonomic keys.
http://ctap.inhs.uiuc.edu/dmitriev/

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.
http://phylogeny.arizona.edu/macclade/macclade.html

Mesquite
Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
http://mesquiteproject.org/mesquite/mesquite.html

MrBayes
Open source software for estimation of phylogenies using Bayesian inference.
http://mrbayes.csit.fsu.edu/

NONA
Freeware software for phylogenetic analyses using parsimony.
http://www.cladistics.com/aboutNona.htm

NONA - A Quick Guide to the Commands
A brief overview of using NONA for phylogenetic analysis.
http://www.gwu.edu/~clade/faculty/lipscomb/Nonadoc.html

PAML
Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
http://abacus.gene.ucl.ac.uk/software/paml.html

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.
http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/

Phylo-Win
Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.
http://pbil.univ-lyon1.fr/software/phylowin.html

r8s
Open source software for estimating absolute rates of molecular evolution and divergence times on phylogenetic trees.
http://loco.biosci.arizona.edu/r8s/

SuperTree
Implements various supertree building methods. Available in Linux/Unix and PC versions.
http://www.tcd.ie/Botany/NS/SuperTree.html

Tree Puzzle
Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
http://www.tree-puzzle.de/

TreeMap
Experimental program for comparing host and parasite trees.
http://taxonomy.zoology.gla.ac.uk/rod/treemap.html

TreeView
Simple program for displaying phylogenies.
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html