Dear members,

I have done a multiple sequence alignment of amino acid using MAFFT program. Then, I would like to find a similarty score againt each alignment. For the example, The file contained tree sequence. i expect to find a sequence similarty matrix of sequence1 with sequence 2 , sequence 1 with sequence 3, sequence 2 with sequence 3.

I found a very useful web-based tool, SIAS (http://imed.med.ucm.es/cgi-bin/sias_new.cgi?jobid=1492116771). However, I would like to analyze using the python or R command line due to a number of large data. I would greatly appreciate if you can give suggestions.

Thank you very much, Ping