What would you say is the best Maximum Parsimony method/software to use? I'm going to use to make a comparison between this and Maximun Likelihood (RAxML).
I generally advise against parsimony, but I guess if it could be a useful form of comparison. Two software choices come to mind immediately: PAUP* (http://paup.sc.fsu.edu/downl.html) and TNT (http://www.zmuc.dk/public/phylogeny/tnt/). PAUP* used to require a license, but I'm not sure if this is still the case. TNT is free. Both are run through a command line interface.
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