As I understand it at present there is no reliable way of taking gaps into
account in an
analysis. In the gap regions the alignment is more uncertain - for this
people choose to remove the gap regions from their dataset. You can do this
in a program like BioEdit, or you can use PAUP and the exclude command to
which columns you want to exclude from your dataset.
Hope that helps,
University of York
Tilman Lamparter wrote:
> 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 zedat.fu-berlin.de>> ---