how to treat gaps in alignments for distance calculations?

Tilman Lamparter lamparte at
Fri Oct 25 04:23:28 EST 2002

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.

Tilman Lamparter
Freie Universitaet Berlin, Pflanzenphysiologie
Koenigin Luise Str. 12-16, D-14195 Berlin
e-mail lamparte at


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