DNA substitutions saturated?

Mark Siddall mes at zoo.toronto.edu
Fri Dec 1 20:30:08 EST 1995

This is in response to Doug Eernisse's post.
(Hi Doug!).
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

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