Running Muscle3D with ensembles

[pentamorfico]

Hi!

I would like to run Muscle 3D with the ensembles method. Is there a way to do it in the current version?

I'm trying to run:

muscle -super7 structs.mega -diversified -distmxin structs.distmx -output structs.afa

But I get the following message:

WARNING: Option -diversified not used

Thanks in advance!

[rcedgar]

Unfortunately super7 does not support ensembles with version ≤ 5.3. Probably not helpful for your case, but for the record ensembles with structures should work with align.

[pentamorfico]

Hi Robert! Thanks for your reply!

Is there a way to replicate the ensemble diversification explicitly (the exact perturbations, random seeds, guide-tree tweaks, or other settings that -diversified uses) so I can launch multiple independent runs in parallel on an HPC system with the -align command? Any pointers to the precise parameters MUSCLE varies under -diversified would be very helpful.

Thanks so much in advance, Mario

[rcedgar]

It's explained here: https://drive5.com/muscle5/manual/diversified_ensemble.html, as seen in the the figure by default a diversified ensemble uses random number seeds 1 .. 100 (-peturb option) while cycling through the 4 guide tree variants (-perm option none | abc | acb | bca)