[Taxacom] Felsenstein lecture available on-line

Dr. David Campbell amblema at bama.ua.edu
Fri Dec 5 16:39:01 CST 2008

Quoting Louise Crowley <crowley at amnh.org>:

> It is hardly the fault of POY that someone inadvertently or otherwise
> did not blast their sequences prior to analyzing them in POY. 
> Whether  
> you choose to analyze dynamically with POY or statically with some  
> other phylogenetic program, a bacterial sequence included in an  
> analysis of Molluscan taxa is bound to give a curious result.
True, it is a user error, not a program flaw.  The only reason why the 
problem is more likely to occur with something like POY is because you 
don't have to look at the sequence before running an analysis (though 
you ought to), whereas if you do an alignment you will probably notice 
if a sequence is so divergent as to be hard to align.  
I have, however, seen a published alignment of paralagous introns that 
did not appear to have any significant similarity-just because an 
alignment program gives output doesn't mean that it's meaningful.  

Dr. David Campbell
425 Scientific Collections Building
Department of Biological Sciences
Biodiversity and Systematics
University of Alabama, Box 870345
Tuscaloosa AL 35487-0345  USA

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