Where is protml (Phylip) ?

[Frank Wright]

PHYLIP 3.5 includes PROTML (from the MOLPHY package) because v 3.5 does
not have a protein maximum likelihood program.

However, PHYLIP 3.6 (almost about to go to a Beta release) has a new
program, PROML, which is a PHYLIP protein maximum likelihood program. 
PROML has additional features to PROTML.  

I suggest waiting for PHYLIP 3.6 to be released and EMBOSS/EMBASSY is
adapted to access v 3.6 programs.  In the meantime, PHYLIP 3.6 (alpha
version, but pretty stable) is available from
http://evolution.genetics.washington.edu/phylip.html.

Best Wishes,
Frank
-- 
Frank Wright
Biomathematics and Statistics Scotland, 
SCRI, DUNDEE DD2 5DA, Scotland
frank at bioss.sari.ac.uk