[Taxacom] Morphology vs Molecular

[Bob Mesibov]

Hi, Brian.

I agree, what you do with your sequence data (i.e., what analysis you do to what end) and how well you know your sequences in advance could determine whether you include or exclude various bits.

Alternatively, you can include and exclude and compare, just to see what happens. I've done this myself when re-analysing published relationships from the original GenBank sequences, using the splits network program SplitsTree4. This program generates networks with or without gap sites, constant sites and parsimony-uninformative sites, and also allows user-defined character filtering.

In the cases I've looked at, where the published arthropod trees had some very old nodes, it didn't make much difference what you did with gaps. There was so much evolutionary noise in the network that you were never going to get a well-resolved picture. You would know better than me how often this is the case with prokaryotes.
-- 
Dr Robert Mesibov
Honorary Research Associate
Queen Victoria Museum and Art Gallery, and
School of Zoology, University of Tasmania
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
(03) 64371195; 61 3 64371195
Website: http://www.qvmag.tas.gov.au/mesibov.html