- Component
http://taxonomy.zoology.gla.ac.uk/rod/cpw.html
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.
- GeneTree
http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.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 web page. Available for Macintosh and Windows.
- MacClade
http://phylogeny.arizona.edu/macclade/macclade.html
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.
- PAUP*
http://paup.csit.fsu.edu/
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.
- PHYLIP
http://evolution.genetics.washington.edu/phylip.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, and runs on most platforms.
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Alignment Software
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