I am looking for the pairwise sequence alignments of a collection of proteins, and I want the alignment scores in matrix format. How can I get pairwise alignment score matrix using T-Coffee or other alignment programme?
I think you need to provide us with a bit more detail. Do the proteins all belong the same family so that you can make a multiple alignment, based on which you would then extract the similarity/distance between any two proteins.
Proteins belongs to two species of Bacteria
The canonical answer would be to use the phylip package protdist. The EMBOSS package might be easier to use http://emboss.bioinformatics.nl/cgi-bin/emboss/help/fprotdist
I'd do the same if the sequences are aligned.
The pairwise alignment scores used by alignment programs are usually worse than the ones derived from the alignment.
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