phylogenetic tree software?

dstoltz at dstoltz at
Wed May 12 19:53:53 EST 1993

I am looking for software that will assist in the construction of
phylogenetic trees.  At the present time, I have a number of
sequence alignments (both nucleotide and peptide)  that have been 
created using the PILEUP feature of the GCG package.  Unfortunately,
GCG appears to lack any algorithms for tree construction.  In particular,
sources for an implementation of Feng and Doolittle's distance matrix
method would be appreciated (we run VMS on a Vax8000).  I am aware that
new methods have come along (parsimony based/split decomposition analysis/
etc), but I know little regarding the advantages/disadvantages of these
methods.  Any suggestions on the most up-to date methods would be
appreciated.  Also, any comments on the advantages of a rootless vs.
rooted phylogenetic trees would be appreciated.  If it of any help,
the alignments have been performed on the RNA polymerase coding region
of several + strand RNA viruses, ranging from HepA to several plant
Comoviruses and an insect picornavirus like particle.
It would also be helpful (but not vital) if any recommended software
knows how to read the GCG format.

Thanks in advance

Paul Fawcett, Dept of Microbiology, Dalhousie University, Halifax, Canada

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