Entering edit mode
5.0 years ago
Dray
▴
30
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!
Clustal-Omega or T-Coffee =) 10 years ago they were great...
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