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SuperTree
Implements various supertree building methods. Available in Linux/Unix and PC versions.
http://www.tcd.ie/Botany/NS/SuperTree.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/phylowi...
Nona - A Quick Guide to the Commands
A brief overview of using Nona for phylogenetic analysis.
http://www.gwu.edu/~clade/faculty/lipscomb...
TreeView
Simple program for displaying phylogenies.
http://taxonomy.zoology.gla.ac.uk/rod/tree...
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/macc...
RadCon
A package implementing a wide range of consensus methods, including reduced consensus, and for calculation of MRP supertrees. Currently only available for Macs.
http://taxonomy.zoology.gla.ac.uk/~jthorle...
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/j...
Mesquite
Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
http://mesquiteproject.org/mesquite/mesqui...
Tree Puzzle
Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
http://www.tree-puzzle.de/
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/gene...
TreeMap
Experimental program for comparing host and parasite trees.
http://taxonomy.zoology.gla.ac.uk/rod/tree...
3I - Internet-accessible Interactive Identification
Program to create internet-accessible interactive taxonomic keys.
http://ctap.inhs.uiuc.edu/dmitriev/3i.asp
PAML
Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
http://abacus.gene.ucl.ac.uk/software/paml...
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.
http://taxonomy.zoology.gla.ac.uk/rod/cpw....
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2006