Getting foldmason aa.fa, ss.fa, and .nw files when running Foldseek locally

[khabj-snek]

Hi - thanks for creative well functioning software!

I'm running foldseek on the server and get the very useful foldmason_aa.fa, foldmason_ss.fa, and foldmason.nw files available for download. This enables me to look at not only one cluster, but neighbouring clusters. However, I need to run 2000 sequences, which the server can't handle.

When running the 2000 sequences locally, I get the files described on github (res_all_seqs.fasta, res_cluster.tsv, res_rep_seq.fasta).

Is it possible to get the aa.fa, ss.fa, and .nw files when running locally?

I've been looking into the --alignment-output-mode INT option, but with no success.

Thanks for all your work!

[gamcil]

Hi, thanks for using the tools. Are you using Foldseek here? Foldmason should produce those files by default, e.g.
foldmason easy-msa pdbs/ result tmp/ will align all structures in pdbs/ and generate result_aa.fa, result_3di.fa and result.nw. You can also add --report-mode 2 to produce a HTML file with a local version of the webserver output (result.html).

[khabj-snek]

Hi, thanks for your reply. I was using foldseek. When my inquiry was moved to foldmason, I realised it was a separate software. Now, everything works like a charm. Thanks!