PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a program for phylogenetic analysis using parsimony, maximum likelihood, and distance methods. The program has a selection of analysis options and model choices, and accommodates DNA, RNA, protein and general data types. It has options for dealing with phylogenetic trees including importing, combining, comparing, constraining, rooting and testing hypotheses.
Maddison, David R., Swofford, David L. and Maddison, Wayne P. 1997. NEXUS: an extensible file format for systematic information. Systematic Biology 46: 590-621