I am looking for a sequence alignment software capable of pairwise alignment of a large number of protein sequences (10^7).

I tried to go for mpiblast: https://wiki.canterbury.ac.nz/display/UCHPC/Installing+mpiBLAST

but seems their website was down.

Do you know any alternatives to mpiblast which is also highly efficient in protein sequence alignment?



1 Answer 1


The Diamond protein aligner is a very popular tool for pairwise protein alignment which is much faster than blastp while having comparable sensitivity. Diamond also supports the use of using multiple compute nodes (similar to mpiBLAST). You can view the details of the new Diamond 2.0 release in this recent Nature Methods paper (source of the image as well).

...we aligned all 281 million protein sequences from the NCBI nr database against the UniRef50 database, which consists of 39 million sequences, using DIAMOND (v2.0.7) in ultra-sensitive mode...

enter image description here

  • $\begingroup$ Throckmorton thanks a lot for the suggestion! I'll have a look at this aligner now. $\endgroup$
    – Johnny Tam
    Commented Sep 15, 2021 at 1:06

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