[Taxacom] base alignment

[Karl Magnacca]

On 29 Aug 2006 at 9:28, John Grehan wrote:
> > But for
> > everybody I know "phenetic" means classifying on the basis of overall
> > similarity of taxa, not selecting compatible characters.
> 
> I agree with this definition. And according to that definition cladistic
> analysis of molecular characters appears to be an analysis of characters
> established through overall similarity of base substitutions and gaps.

How ya figure?

All the molecular cladists I know (myself included) would be very 
surprised to hear that they have been doing phenetics all these years.  
I guess they wasted all that time aligning sequences in order to 
establish homologies.  I think Dave Swofford would also be interested to 
hear that parsimony becomes phenetic when run on a molecular matrix.

Karl
=====================
Karl Magnacca
UC-Berkeley, ESPM Dept.
137 Mulford Hall #3114
Berkeley, CA 94720


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