I've recently been using the PHYLIP package (v 3.5) to construct trees
based on protein sequence divergences, and the PROTML program seems to
be the ticket.
However, I've had problems getting it to run on my SGI (IRIX 5.0)
system. From what I can make out of the source code (I taught myself
small amounts of PASCAL a long, long time ago) it seems to require an
input file called 'seqdata'; however, when I run the program it doesn't
seem to be able to read in this file.
Does anybody have any experience in getting this program to run under
Bernard Khoo Wellcome/CRC Institute, Cambridge, UK.
bcek1 at cus.cam.ac.uk or @mole.bio.cam.ac.uk