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soedinglab / MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite
https://mmseqs.com
MIT License
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Use MMSeqs to Output full MSA #843

Open d8vela opened 6 months ago

d8vela commented 6 months ago

I'm trying to get mmseqs to output a full global multiple sequence alignment. So far, when I use the cluster mode, it gives me the MSA, but with parts with edges sequence gaps (normally in the N- and C-terminals trimmed off). Is there a way to get all the sequences aligned as the output just like a normal MSA? I want to get a MSA from mmseqs not and export the sequences and run an external MSA program (like ClustalOmega) to do it.

Thanks!

milot-mirdita commented 6 months ago

We don't implement any global MSA algorithms in MMseqs2.

You can use the mmseqs apply module to call external tools directly on MMseqs2 databases (https://github.com/soedinglab/MMseqs2/wiki#how-to-run-external-tools-for-each-database-entry). I recommend FAMSA for MSAs.