[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
