How to calculate all vs all sequence divergence from an alignment? · Biostar

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How to calculate all vs all sequence divergence from an alignment?

Dear Fellow members

I have a query today regarding sequence alignment divergence scoring. I have around 1300 sequence which were aligned with mafft. Now I would like to calculate pairwise sequence similarity percentage between all sequences with respect to all like 1vs2, 1vs3, 1vs4, 2vs1,2vs3,2vs4 and so on. Manually if I try on jalview it will take more than five days to finish all combinations. At the same time I am not getting any other idea. Is there anyway to finish this with R or Perl script?

Thank you

r alignment perl

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written 9.7 years ago by ThulasiS

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