availability of fast phylogenetic tree codes
gonnet at inf.ethz.ch
Fri Dec 11 15:31:46 EST 1992
In article <9212101644.AA15862 at t13.lanl.gov> asl at T13.LANL.GOV (Alan Lapedes) writes:
>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).
Our automatic server implements a basic tree (Felsenstein's algorithm)
with several optimizations. People are generally happy with the trees
(1) - it is written in Darwin, which is written in C.
(2) - not for all nodes, only for the root of the tree
(3) - only peptides
(4) - no problem, we have tried it with more than 500 sequences
(5) - Depends on what you consider fast. For a tree with n sequences
most of these algorithms are O(n^3) so it depends heavily on
the number of sequences.
You can make up your own mind on the quality of the trees and
on the speed by using the automatic server. Send a message with
"help AllAll" as body to cbrg at inf.ethz.ch. If you like it, you can
obtain your own copy of Darwin.
Gaston H. Gonnet, Informatik, ETH Zurich.
More information about the Bio-soft