For easy-cluster how to specify --alignment-type?

[linda5mith]

Forgive me if this is a silly question but in the documentation it says "important cluster parameters": --alignment-type ...

However when I try to specify --alignment-type using easy-cluster I get:

Unrecognized parameter "--alignment-type". Did you mean "--alignment-mode" (Alignment mode)?

Command I'm running: foldseek easy-cluster -c 0.9 ../pdbs_to_TM_align/ res tmp --alignment-type 1

I'm trying to cluster my pdbs using TM-align (--alignment-type 1). Am I missing something?

Many thanks!

[martin-steinegger]

@linda5mith we did not implement --alignment-type in the clustering workflow. However, you can apply --tmscore-threshold to apply TMscore.