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.eduhttp://radon.gas.uug.arizona.edu/~bernster
