I need to find pairwise alignment scores for 10,000 amino acid sequences that range from 200 aa to 4000 aa. I am currently using the EMBOSS wrapper within python to do the comparisons. However, judging by the rate at which the alignments are being performed it will be quite a long time (roughly 2,000 days) before the whole batch is complete. This seems very high and I am guessing there is a better way to accomplish what I am setting out to do.

What I have tried already:

I have excluded any comparisons that cannot generate an identity higher than 50% based on length.