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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 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 settings to tune the 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 current platform GUIs such as Windows 8 and Max OS X, usage as a command line tool is advised.

References

http://paup.csit.fsu.edu/
– Swofford, 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 6 June 2014, but no longer accessible 27 October 2015.

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