Program for aligning coding sequences?

walker at nlm.nih.gov walker at nlm.nih.gov
Mon Oct 26 18:03:51 EST 1998


[posted and mailed]

[F.Schaap at FYS.UNIMAAS.NL writes]
> 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.).

The script

  gap_cds

included in the SEALS package

  http://www.ncbi.nlm.nih.gov/Walker/SEALS

will align coding sequence based on an amino-acid alignment.  The aa
alignment must be in 'aligned fasta' format but can be easily converted
from other common formats.

Write me via email if you have any questions.

R


-- 

Roland Walker
walker at ncbi.nlm.nih.gov
National Center for Biotechnology Information




More information about the Mol-evol mailing list