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steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.
https://foldseek.com
GNU General Public License v3.0
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Question: alignment as FASTAs in plaintext? #149

Open gph82 opened 1 year ago

gph82 commented 1 year ago

Great software!

Is there a way to retrieve the alignments as plaintext FASTAs other than retrieving them from the html output?

Thanks!

martin-steinegger commented 1 year ago

Thank you. Yes, you can use easy-serach ... --format-output query,target,qaln,taln to print the alignment strings TSV formatted (see format options). Alternatively, you can print query and target start position and the cigar string using the output fields qstart,tstart,cigar.