How are gaps to be treated when aligned protein sequences are taken to
obtain distance matrices? Should the regions be excised in all sequences?
I use the Phylip protdist program with Jones-Taylor-Thornton model or
Dayhoff PAM matrix. I always get different results when alignments with
and without gaps are compared.
Freie Universitaet Berlin, Pflanzenphysiologie
Koenigin Luise Str. 12-16, D-14195 Berlin
e-mail lamparte at zedat.fu-berlin.de