This is in response to Doug Eernisse's post.
You asked about something to do with "How to deal with gaps in the alignment".
I'd like to follow this thread here by inquiring of the
readership how they feel about the 2 propositions:
1) indel events are not observed data (that is one does not
observe gaps in a sequence), they are matter of inference, thus, should
not be treated as observed data points (i.e., code them as "missing").
2) in order to achieve a multiple alignment, one must assign a cost
to a gap (or string thereof), thus phylogenetic analysis of he
aligned data without coding for gaps is inconsistent with the
epistemology of having gotten the alignment itself. (Can't have your
cake and eat it too).
A caveat regarding #1 is that even though one is coding it as "missing"
it will be assigned a nucleotide state in searches (just whatever is
most optimal), and yet, this contravenes the fact that there is no state
to be had.
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