I am interested in obtaining one or more phylogenetic tree codes that implements
a conventionally accepted algorithm for producing trees. Apparently,
phylogenetic tree algorithms seem to be a somewhat controversial topic -- hence
my request for code that, even if not universally accepted, has at least been
analysed and debated in the literature.
(1) Would prefer C, Fortran is OK.
(2) Would like to be able to produce not only trees, but also a
parsimonious reconstruction of the sequences at the nodes.
(3) Would like to be able to handle either nucleotides, or amino acids as input.
(4) Would particularly like to be able to handle a few hundred amino acid
sequences, up to a couple of hundred residues long as input.
(5) It's critical to us to have reasonable speed: in our admittedly naive hands
the "protpars" code for a problem the size of point (4) above takes too
(6) If the code is in C or Fortran we could possibly run it on supercomputers
for a speed-up. If the code is already ported to vector or parallel
machines we would appreciate information on acquiring the code, or accessing
the machine (if a service is provided).