protein based nucleotide multiple alignments

[Thorsten Burmester]

Dan wrote:

> Hi Everyone, after trying to find an program to align multiple
> nucleotide sequences based on a protein multiple alignment I have given
> up and written one for myself using perl. 

Did you check GeneDoc? http://www.psc.edu/biomed/genedoc/

This nice litte program does exactly what you want.

> The program allows you to get
> around the problems of optimal nucleotide alignments that are unlikely
> to be evolutionarily significant due to matches in adjacent codons in
> protein coding sequeces. I'd like to write it up somewhere, but I have
> no idea where to find references that say that this kind of thing is
> important.
> Does anyone have any idea where I would find this (or if it exists)?

Maybe it's a good idea to check the GeneDoc manual or to contact the
authors. 

HTH,

Thorsten

-- 
Thorsten Burmester
thorsten at erfurt.thur.de
http://www.uni-mainz.de/FB/Biologie/Zoologie/abt2/thorsten/thorsten.htm