PAUP*
Computational phylogenetics program
title: "PAUP*" type: doc version: 1 created: 2026-02-28 author: "Wikipedia contributors" status: active scope: public tags: ["phylogenetics-software"] description: "Computational phylogenetics program" topic_path: "science/biology" source: "https://en.wikipedia.org/wiki/PAUP*" license: "CC BY-SA 4.0" wikipedia_page_id: 0 wikipedia_revision_id: 0
::summary Computational phylogenetics program ::
::data[format=table title="Infobox software"]
| Field | Value |
|---|---|
| name | Phylogenetic Analysis Using Parsimony *****and other methods |
| logo | File:Pauph.gif |
| screenshot | |
| author | David L. Swofford |
| released | |
| latest release version | 4.0b10 |
| latest release date | |
| latest preview version | 4.0a164 |
| latest preview date | |
| programming language | C |
| operating system | Windows, macOS, Unix-like |
| platform | Cross-platform |
| genre | Science |
| license | Quasi-commercial |
| website | |
| :: |
| name = Phylogenetic Analysis Using Parsimony *****and other methods | logo = File:Pauph.gif | screenshot = | caption = | collapsible = | author = David L. Swofford | developer = | released = | discontinued = | latest release version = 4.0b10 | latest release date = | latest preview version = 4.0a164 | latest preview date = | programming language = C | operating system = Windows, macOS, Unix-like | platform = Cross-platform | size = | language = | genre = Science | license = Quasi-commercial | website =
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, with which it shares the NEXUS data format, PAUP was the phylogenetic software of choice for many phylogenetists.
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, in addition to parsimony, likelihood, and distance methods for phylogenetics.
References
References
- (2001-02-08). "MacClade 4: Analysis of Phylogeny and Character Evolution".
- (December 1997). "NEXUS: an extensible file format for systematic information". Systematic Biology.
- (2001). "Phylogenetic Trees Made Easy". Sinauer Associates.
- (December 2014). "Quartet inference from SNP data under the coalescent model". Bioinformatics.
- (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.
::callout[type=info title="Wikipedia Source"] This article was imported from Wikipedia and is available under the Creative Commons Attribution-ShareAlike 4.0 License. Content has been adapted to SurfDoc format. Original contributors can be found on the article history page. ::