NA vs. AA phylogenies

Ulrich Melcher umelcher at bmb-fs1.biochem.okstate.edu
Wed Jan 17 09:51:13 EST 1996


	    Molecular phylogenies can be constructed from optimal 
(algorithm-defined) alignments of amino acid sequences or of nucleotide 
sequences.  Some folks construct phylogenies based on each.  The two 
phylogenetic trees may differ from one another.  Novices will often 
interpret these differences with regard to coding vs. non-coding 
changes, while experts will recognize that the alignments on which the 
trees are based are not necessarily equivalent.

     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 bmb-fs1.biochem.okstate.edu
Department of Biochemistry     
  and Molecular Biology        Tel: 405-744-6210
246 NRC                        FAX: 405-744-7799
Oklahoma State University
Stillwater OK 74078-3035 USA





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