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Multiple Sequence Alignment Score

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..

multiple
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updated by zx8754 zx8754 • written by User 0431 • User 0431

3 answers

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.

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written by Jorge Amigo Jorge Amigo

A start could be Sean Eddy's squid library (superseded by easel now).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

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written by Andreas Andreas

thank so much for your help andreas and Jorgo, I will try look at both of them and let you know if that solve my problem..or ask your help again

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written by User 0431 • User 0431

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