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

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

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 diag
   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

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

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/

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

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