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.

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.

Phylogenetic analyses of DNA or protein sequences using maximum likelihood.

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

Software for creating taxonomic keys.

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

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