I wonder if anyone knows whether any of the phylogeny packages
available (or just a single program) can allow one to test whether
the most parsimonious tree is significantly better than alternative
topologies statistically for protein sequence data using a method
which does NOT employ the stepmatrix in PROTPARS to calculate the
number of steps for the given tree. In essence I wish to do
protein parsimony without any stepmatrix and decide between the
best tree and some alternative trees. I'm relatively poor at
math so I haven't been able to understand the methods described by
Kishino and Hasegawa, (1989), 29:170-179 J. Mol. Evol. and figure
out how they apply to protein sequence data.
Any simple answers will be appreciated!
Dept. of Biochemistry
aroger at ac.dal.ca