Multiple Sequence Alignment Score

Question

[User 0431]

I m looking for a source code that can take multiple sequence alignment and return back the Sum-of-pairs or weight sum-of-pairs score based on any scoring scheme.. any one can help..

Answer 1

[Jorge Amigo]

when I moved on from CLUSTAL, I found MAFFT to be a great (and amazingly faster) alternative for multiple sequence alignment that even allowed to play around with scoring matrices. I know it takes sum-of-pairs into account when setting up a run, but what I don't know is if it provides them as output. the source is available and published, so I think it would be worth it giving it a try.

Answer 2

[Andreas]

A start could be Sean Eddy's squid library (superseded by easel now). When you compile the source you get - among other tools - one binary which is called alistat. It computes an average pairwise identity (simply 1 for match, 0 for mismatch) of sequences in the alignent. Have a look at alistat_main.c.

If you need something more sophisticated have a look at the source code of Muscle. It can for sure score your alignment in different ways. I can't find the appropriate function at the moment but check all files starting with dist*.

Andreas