Does any one know the particular weighting matrix used by the Gap
program in the GCG package? I am having difficulty reproducing some
published alignments based on that program utilizing alternative
alignment progs such as Genalign, Clustalv etc. which allow for
PAM 250, 100 and Identity matrices. If indeed another form of
weighting matrix is used in GCG Gap, is there a published reference
in which a description and justification exists?
Thanks.
mark-b at molbio.cbs.umn.edu
