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
basis.
I am interested in the nucleotide sequences here, not the amino acid
sequences.
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?
Thank-you,
Tom Isenbarger
---
