PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a program for phylogenetic analysis using parsimony, maximum likelihood, and distance methods (Swofford 2003). The program features an extensive selection of analysis options and model choices, and accommodates DNA, RNA, protein and general data types. Among the many strengths of the program are the rich array of options for dealing with phylogenetic trees including importing, combining, comparing, constraining, rooting and testing hypotheses.
Downloads for PAUP* test versions can be found here: http://people.sc.fsu.edu/~dswofford/paup_test/
Example NEXUS Files
- Cat data (view, download)
- Primate data (view, download)
- Real data (view, download)
- Simulated data (view, download)
Example PAUP blocks
- ML heuristic search (view, download)
- Constraint tree (view, download)
- Hypothesis testing (among trees) (view, download)
Additional sample files are available on the PAUP* web site, including amino acid alignments and DNA alignments with definition of codon positions.
A brief description of the likelihood ratio test is available locally. For online PAUP support go to the PAUP* Support Web pages (includes FAQ, Command Reference Document, Sample NEXUS files, Helpful Links).
All versions of PAUP* require data and commands to be present in NEXUS format (with the exception that commands can additionally be executed interactively from the command prompt). PAUP* is run by entering the command
paupFrom the command line, NEXUS files are executed by including the filename: