NA vs. AA phylogenies

Joe Felsenstein joe at
Wed Jan 17 16:58:16 EST 1996

In article <4dj2d1$1t2 at>,
Ulrich Melcher  <umelcher at> 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 

You might want to look at the papers by Jotun Hein and J. Stovlbaek:

Hein-J.  Stovlbaek-J.
Genomic alignment.
J-Mol-Evol.  1994 Mar.  38(3).  P 310-6.

An algorithm combining DNA and protein alignment.
J-Theor-Biol.  1994 Mar 21.  167(2).  P 169-74.

Hein-J.  Stovlbaek-J.
A maximum-likelihood approach to analyzing nonoverlapping and
overlapping reading frames.
J-Mol-Evol.  1995 Feb.  40(2).  P 181-9.

Joe Felsenstein         joe at     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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