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more ?s on alignments and S/NS substitutions

Thomas Isenbarger isen at molbio.mgh.harvard.edu
Fri Jan 30 16:30:25 EST 2004

Hello all:

I have a clustalw alignment of homologous nucleotide sequences from 5
microbial genomes.  I want to quantify the synonymous/nonsynonomous
substitutions along the length of the alignment on a codon-by-codon

I am interested in the nucleotide sequences here, not the amino acid

1.  can anyone suggest a method (freely available software would be nice
too) for aligning the nucleotide sequences using the translated amino
acid sequence as a guide?  if not, can anyone recommend an alignment
viewer for multiple alignments that allows one to view both the
nucleotide sequence and translation simultaneously for all sequences in
the alignment? (so I can adjust the nucleotide alignment by hand)

then, can anyone suggest good software for processing the alignment to
do the substitution quantification I mentioned above?

Tom Isenbarger

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