<p> 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..</p>

<p>when I moved on from CLUSTAL, I found <a href="http://mafft.cbrc.jp/alignment/software/">MAFFT</a> 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.</p>