NA vs. AA phylogenies

ggutman at VMSA.OAC.UCI.EDU ggutman at VMSA.OAC.UCI.EDU
Wed Jan 17 11:25:36 EST 1996

On Wed, 17 Jan 1996, Ulrich Melcher 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?
>      If such software does not exist, should it?
> Ulrich Melcher                 umelcher at
> Department of Biochemistry     
>   and Molecular Biology        Tel: 405-744-6210
> 246 NRC                        FAX: 405-744-7799
> Oklahoma State University
> Stillwater OK 74078-3035 USA


I have DOS software which will take an amino acid sequence alignment
(CLUSTAL format) and replace it with the corresponding nucleotide
sequences, presuming these are available.

The second job you describe is not generally possible, since nucleotide
sequence alignments do not observe codon boundaries.


* George A. Gutman                                              *
* Department of Microbiology            Tel:(714)824-6593       *
*          and Molecular Genetics       FAX:(714)824-8598       *
* University of California         INTERNET: GAGUTMAN at UCI.EDU   *
* Irvine CA 92717                                               *

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