Can anyone suggest a sane-to-use and reasonably fast implementation of parsimony tree estimation for DNA sequences that returns ancestral sequences as well? We have been using PHYLIP’s
dnapars but getting all the information out of its output files is pretty hairy.
@NickJMatzke has (partially?) written http://phylo.wikidot.com/tntr as an R front-end to the TNT software, but this also looks pretty wild!
Yes, parsimony .