Fast all to all global alignment

Question

[Dray]

I need to perform a global all to all sequence alignment of 10k sequences (this needs to be done for many datasets, sequence lengths 150-300aa). Currently the fastest way I could find is to use emboss needleall, however it still takes >10 hours per dataset. Would be great if anyone would share a faster solution!

[German.M.Demidov]

Clustal-Omega or T-Coffee =) 10 years ago they were great...

[gb]

USEARCH: https://drive5.com/usearch/manual/cmd_allpairs_global.html

VSEARCH: https://github.com/torognes/vsearch

Sorry, wrote this comment before but removed it unintentionally

Answer 1

[lagartija]

What kind of alignment ? What for ? The first software I would suggest is diamond