You should really use the similarity measure that pertains to what you want to investigate and situation rather than what is most commonly used.
All the similarity measures you've listed essentially come from the same score calculated from the best alignment according to a scoring matrix. The different measures are just the score normalized or scaled differently. Here is the [?]NCBI explanation[?] for the similarity scores you've listed.
The pairwise2 module uses a standard dynamic programming algorithm which uses a scoring matrix. I would read up on how dynamic programming is used for sequence alignments. Start with the wikipedia entry on [?]sequence alignment[?] and go from there.
Personally, I would use a bit score as it is independent of the substitution matrix and search space.
modified 8.3 years ago
8.3 years ago by
Damian Kao ♦ 15k