[Taxacom] base alignment

Karl Magnacca kmagnacca at alumni.wesleyan.edu
Wed Aug 30 01:01:32 CDT 2006

On 29 Aug 2006 at 12:28, John Grehan wrote:
> If I am wrong then fine. I am just giving my impression of what I have
> read so far. For example, one paper I read stated that alignment uses
> distance measures which to my understanding is not cladistic.

Don't forget that in most cases of coding genes and even many introns, 
alignment is not necessary or trivial (i.e. it's the difference between 
90% similarity in the correct alignment and 30% similarity when not 
properly aligned).  It's mainly ribosomal genes that have such problems 
with alignment, which is why they are falling out of favor as more 
nuclear genes are developed for more taxa.

> None of this means that molecular people have necessarily been wasting
> their time. I am not saying that molecular trees cannot be correct, just
> that they are not necessarily correct just because they use DNA
> sequences, and that morphology is not necessarily wrong when it does not
> corroborte molecular trees.

That is certainly true, but not for reasons that have anything to do 
with the "cladisticness" of their methods.

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

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