create phylogeny from clustering structures

[avilella]

is there a way to create a phylogeny from clustering structures rather than sequences?

I've successfully run:

foldseek createdb example/ db
foldseek search db db aln tmpFolder -c 0.8 
foldseek clust db aln clu
foldseek createtsv db db clu clu.tsv

But I would like to obtain a phylogeny output rather than the tsv output file. Is this possible? Thx

[martin-steinegger]

To utilize the taxonomy features in MMseqs2/Foldseek, you must first label the sequences in your database with taxonomy IDs. You can find detailed instructions on how to do this in our user guide wiki: https://github.com/soedinglab/MMseqs2/wiki#taxonomy-assignment. I recommend posting this question on the FoldSeek GitHub page. :)