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PAUP (Phylogenetic Analysis Using Parsimony) is a proprietary, and thus commercial, non-free software package for constructing and interpreting phylogenetic trees. It can is able to apply a maximum parsimony method, but also various others methods (that may, however, be less suitable to stemmatological analysis). It offers a rich set of commandos settings to tune the behavior behaviour of various methods, and to adapt the lay-out of computed trees. PAUP uses the Nexus file format which is shared by several bioinformatics software packages. Different versions for various platforms are available , with slight variations in available functionality. PAUP can both be used as a command line tool or through a graphical interface. However, given lack or incomplete support for later current platform GUIs such as Windows 8 and Max OS X, usage as a command line tool is advised.

References

- http://en.wikipedia.org/wiki/PAUP
- http://paup.csit.fsu.edu/
- Swofford, D. David L., 2002. PAUP*. : Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4, beta version. Sunderland: Sinauer Associates. Available at http://www.tsu.edu/PDFFiles/CBER/Miranda/PAUP%20Manual.pdf [accessed . Accessed 6 June 2014]

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, but no longer accessible 27 October 2015.

JZ