PAUP* (Phylogenetic Analysis Using Parsimony and Other Methods) is a powerful, full-featured phylogenetic inference package that incorporates traditional parsimony as well as distance and maximum likelihood methods. It is the world's most widely used suite of tools for phylogenetic inference.

Using PAUP* on HPC

PAUP* is available on all HPC nodes as a command line program. There is no graphical user interface (however, a subset of PAUP* is available in GCG/SeqLab through PAUPSearch/PAUPDisplay). See extensive PAUP* documentation here, plus command line help is available within the package. Also see our miniworkshop for more help on using command line phylogenetic inference software.

Do not run large bootstrap jobs interactively! They will be shut down.

See RepMaker instead and work within the MOAB framework.