PAUP (Phylogenetic Analysis Using Parsimony) is a proprietary, and thus commercial non-free software package for constructing and interpreting phylogenetic trees. It can 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 to tune the behavior 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 platform GUIs such as Windows 8 and Max OS X, usage as a command line tool is advised.
– Swofford, D. 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]