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Phylogenetic Analysis Using Parsimony *and other methods
Original author(s) David L. Swofford
Stable release
Preview release
Written in C
Operating system Macintosh, Windows, Unix-like
Platform Cross-platform
Type science
License commercial
Website PAUP*

PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees (phylogenies), written by David L. Swofford. Originally, as the name implies, PAUP only implemented parsimony, but from version 4.0 (when the program became known as PAUP*) it also supports distance matrix and likelihood methods. Version 3.0 ran on Macintosh computers and supported a rich, user-friendly graphical interface. Together with the program MacClade,[1] with which it shares the NEXUS data format,[2] PAUP* was the phylogenetic software of choice for many phylogenetists.[3] Version 4.0 added support for Windows (graphical shell and command line) and Unix (command line only) platforms. However, the graphical user interface for the Macintosh version requires Classic, which is no longer supported by Mac OS X 10.5 and later. There is a command line version of PAUP* for Intel-based Macs. PAUP* is also available as a plugin for Geneious. The program now sports the self-referential title of PAUP* (* Phylogenetic Analysis Using PAUP).


  1. ^ D R Maddison & W. P. Maddision. MacClade 4: Analysis of Phylogeny and Character Evolution. ISBN 0-8789-3470-7. 
  2. ^ Maddison DR, Swofford DJ, Maddison WP (1997). "NEXUS: an extensible file format for systematic information". Systematic Biology. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. ISSN 1063-5157. PMID 11975335. 
  3. ^ Hall, Barry G. (2001). Phylogenetic Trees Made Easy. Sinauer Associates. ISBN 0-8789-3311-5. 

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