Program for aligning coding sequences?

walker at walker at
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


included in the SEALS package

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.



Roland Walker
walker at
National Center for Biotechnology Information

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