In article <ts15-2306951442190001 at 184.108.40.206>, ts15 at cornell.edu (Ted
> [..."protein Parsimony"] can be
> implemented by generateing a protein parsimony step matrix in MacClade,
> then running the analysis in PAUP after assigning the step-matrix
> character type to the amino acid characters.
PAUP 3.x or greater has always included sample files with "ProtPars" step
matrices for either standard or vertebrate mtDNA codon table
translations. MacClade may allow you to do other nonstardard codes,
for example, fly/mollusc/nematode or echinoderm mtDNA codes -- I'm not
> I understand that protein
> parsimony can also be applied in PHYLIP, though I have never tried this.
I believe the standard ("universal") codon translation protein
parsimony (ProtPars) is used as default, with no option to do parsimony with
equal weighting or protein parsimony based on other codes. One should
still be able to use equal weighting if the data are not treated as
protein data. Is this still correct, Joe?
Doug Eernisse <DEernisse at fullerton.edu>
Dept. Biological Science MH282
California State University
Fullerton, CA 92634