Software:PAUP*
 | |
| 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 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
- ↑ MacClade 4: Analysis of Phylogeny and Character Evolution. 2001-02-08. ISBN 0-8789-3470-7. http://www.sinauer.com/detail.php?id=4707. Retrieved 2015-12-08.
- ↑ "NEXUS: an extensible file format for systematic information". Systematic Biology 46 (4): 590–621. December 1997. doi:10.1093/sysbio/46.4.590. PMID 11975335.
- ↑ Phylogenetic Trees Made Easy. Sinauer Associates. 2001. ISBN 0-8789-3311-5. https://archive.org/details/phylogenetictree0000hall.
- ↑ "Quartet inference from SNP data under the coalescent model". Bioinformatics 30 (23): 3317–24. December 2014. doi:10.1093/bioinformatics/btu530. PMID 25104814.
- ↑ "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. June 2015. doi:10.1016/j.jtbi.2015.03.006. PMID 25791286.
External links
 |
