[BiO BB] clustalw alignment pairwise

Gary Van Domselaar gary at primary.bioinformatics.org
Fri Jul 28 08:29:56 EDT 2006

Hi Daniele,

Clustalw doesnt have a provision for preserving reading frame on 
nucleotide alignments, so what we do is
use an 'align on codons' procedure where we do a multiple alignment on the 
protein translations, then
back translate that alignment in to the original nucleotide sequences.

The freely downloadable windows-based program 'MEGA3' will do this for 


Gary Van Domselaar, PhD
Associate Director, Bioinformatics.Org
gary at bioinformatics.org

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