In article <DEernisse-0312950915140001 at deernisse.fullerton.edu> DEernisse at fullerton.edu (Doug Eernisse) writes:
>alignment is estimated with various algorithms (e.g., Clustal, the
>Malign program by Wheeler and Gladstein) then including the gap matrix
>usually decreased the percentage of replicates where the true tree was
>estimated by parsimony. In other words, as the alignment deteriorates,
>one should become increasingly wary of treating gaps as anything other
>than missing data.
My empirical observations have been similar. What worries me is
the lack of some choice criterion upon which we can make decisions
about including or excluding this information.
Maybe what is needed is something at the alignment stage. That is, if a
gap (or indel event in general) is robust to alignment parameters
it should be coded but otherwise treated as missing.
Mark E. Siddall "I don't mind a parasite...
mes at vims.edu I object to a cut-rate one"
Virginia Inst. Marine Sci. - Rick
Gloucester Point, VA, 23062