PAUP*

Phylogenetic Analysis Using Parsimony *and other methods
Original author(s)	David L. Swofford
Stable release	4.0b10
Preview release	4.0a164
Written in	C
Operating system	Macintosh, Windows, Unix-like
Platform	Cross-platform
Type	science
License	quasi-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 does not support versions of Mac OS X higher than 10.14 (although a GUI for later versions of Mac OS is planned). PAUP* is also available as a plugin for Geneious. PAUP*, which now sports the self-referential title of PAUP* (* Phylogenetic Analysis Using PAUP), is undergoing rapid updates and it now includes the "species tree" method SVDquartets,[4][5] in addition to parsimony, likelihood, and distance methods for phylogenetics.

References

Maddison DR, Maddision WP (2001-02-08). MacClade 4: Analysis of Phylogeny and Character Evolution. ISBN 0-8789-3470-7. Archived from the original on 2011-09-27. Retrieved 2015-12-08.
Maddison DR, Swofford DL, Maddison WP (December 1997). "NEXUS: an extensible file format for systematic information". Systematic Biology. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. PMID 11975335.
Hall BG (2001). Phylogenetic Trees Made Easy. Sinauer Associates. ISBN 0-8789-3311-5.
Chifman J, Kubatko L (December 2014). "Quartet inference from SNP data under the coalescent model". Bioinformatics. 30 (23): 3317–24. doi:10.1093/bioinformatics/btu530. PMC 4296144. PMID 25104814.
Chifman J, Kubatko L (June 2015). "Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites". Journal of Theoretical Biology. 374: 35–47. arXiv:1406.4811. doi:10.1016/j.jtbi.2015.03.006. PMID 25791286. S2CID 17167792.

External links

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[1] Maddison DR, Maddision WP (2001-02-08). MacClade 4: Analysis of Phylogeny and Character Evolution. ISBN 0-8789-3470-7. Archived from the original on 2011-09-27. Retrieved 2015-12-08.

[2] Maddison DR, Swofford DL, Maddison WP (December 1997). "NEXUS: an extensible file format for systematic information". Systematic Biology. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. PMID 11975335.

[3] Hall BG (2001). Phylogenetic Trees Made Easy. Sinauer Associates. ISBN 0-8789-3311-5.

[4] Chifman J, Kubatko L (December 2014). "Quartet inference from SNP data under the coalescent model". Bioinformatics. 30 (23): 3317–24. doi:10.1093/bioinformatics/btu530. PMC 4296144. PMID 25104814.

[5] Chifman J, Kubatko L (June 2015). "Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites". Journal of Theoretical Biology. 374: 35–47. arXiv:1406.4811. doi:10.1016/j.jtbi.2015.03.006. PMID 25791286. S2CID 17167792.