In Article <70vr0v$o79 at net.bio.net>, f.schaap <F.Schaap at FYS.UNIMAAS.NL> wrote:
>Does anyone know of an alignment program which takes into account the fact
>that the input file contains protein-encoding nucleotide sequences? In other
>words some programs where the nucleotide alignment is guided by the amino
>acid alignment (nucleotide gaps are inserted in multiples of three etc.).
Check this web site;
Doug Eernisse has written a hypercard stack that does this, among other
things. What you need is a protein alignment and the coding nucleotide
sequences, and the stack will line up the nucleotide sequences with the
encoded amino acids. The documentation is with the stack. Note, you need
Hypercard, and hence a Mac, to run this one. I've used it for alignments of
up to 18 sequences.
Department of Biological Sciences
University of Alberta
Edmonton, Alberta T6G 2E9
wgallin at gpu.srv.ualberta.ca