Cipres Science Gateway

PAUP is software for inferring phylogenetic trees from matrices based on standard characters, as well as protein and nucleotide sequences. PAUP stands for Phylogenetic Analysis Using Parsimony. It was created by Dave Swofford, and is available for individual licensing through the home page below. We expose here a few of the functionalities of the entire PAUP package, as well as PAUP boosted by Rec-I-DCM3.

A manual for PAUP is available. [pdf]

PAUP home page here.

INPUT = standard, dna, and protein character matrices in Nexus format.

Test input file (12 taxa): PAUP_12Tx432C.nex

Test output file1 (default, but no ratchet): paup_noratchet_outfile.nex

Test output file1 (default; 200 ratchets): paup_200ratchet_outfile.nex

If you use PAUP, please cite: Swofford, D. L. (1991) PAUP: Phylogenetic Analysis Using Parsimony, Version 3.1 Computer program distributed by the
Illinois Natural History Survey, Champaign, Illinois.

If there is a tool or a feature you need, please let us know.