PAUP

PAUP

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 are using the multithreaded version of PAUP, now available as an experimental implementation: see here. Our interface is minimalist by design, because all commands can be accessed through a Nexus PAUP block, but it can easily be expanded, just send us your requests. All runs are allocated 4 threads, which is the optimum for us. If you think you may need more threads, just let us know.

A manual for PAUP is available [pdf]

Current updates on PAUP are available

INPUT = standard, dna, and protein character matrices in Nexus format, with or without commands.

Test input file for an SVD Quartet analysis: snakes.txt; (borrowed from Laura Kubatko's SVD Quartet tutorial at http://evomics.org/learning/phylogenetics/svdquartets/svdquartets_tutorial2015/

Please Note: If you want to obtain good speedup using SVD quartets analysis, you MUST modify the PAUP block of your input file.
The SVDQuartets line must include a statement for the correct number of threads. For example, if you wish to use 16 threads:

SVDQuartets evalQuartets=all speciesTree partition=species bootstrap=standard nreps=100 threads=16;

Without this statement, the app. will use just two threads, but your account will be charged for 16.

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.

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