NA vs. AA phylogenies

R M Bernstein ralph at ccit.arizona.edu
Sun Jan 21 17:30:23 EST 1996


In Article <4du3cd$991 at news.nstn.ca>, "Andrew J. Roger" <aroger at ac.dal.ca>
wrote:

>>     Is there software that can:
>>1) Given an amino acid sequence alignment and the raw nucleotide 
>>sequences that translate to the amino acid sequences, produce a 
>>nucleotide sequence alignment that is equivalent to the amino acid 
>>sequence alignment; and/or
>>2) Given a nucleotide sequence alignment, translate the constituent 
>>sequences into aligned amino acid sequences, so that the resulting amino 
>>acid sequence alignment is equivalent to the nucleotide sequence 
>>alignment?

>My feeling is that currently we have programs which
>use empirically derived substitution matrices for
>amino acids (for distance we can use Joe's PROTDIST,
>for likelihood we can use PROTML or AAML (from Yang's
>PAML program) and thus we are more likely to be 
>basing our analyses on reasonable assumptions about amino
>acid evolution. However, it is common to see the use
>of nucleotide programs with coding sequence. Typically
>people get rid of third base positions for deep
>phylogenetic questions....However, using DNADIST,
>or DNAML with settings meant for non-coding sequences
>(for instance using Kimura's two parameter model with
>a Ts/Tv ratio > 1) I believe to be inferior to using 
>amino acids. 


I would also suggest the new release of GCG which has 2 programs which do
exactly what the first poster asked; they align nucleotide seq with amino
acid seq.  Framealign and framesearch, from the 8.1 release (i think its 8.1)
GCG is in Mad. WI, and even have a home page...url?


Regards, Ralph



R.M. Bernstein
Dept of Micro/Immuno
University of Arizona
Ph: 602 626 2585
Fx: 602 626 2100
url: http://lamprey.medmicro.arizona.edu
     http://radon.gas.uug.arizona.edu/~bernster



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