Robert Edgar

Update -- I was able to work around the problem by removing `alntmscore` from the `format-output` option, I'm guessing computing the TM alignment is much slower than the S-W 3Di...

https://wwwuser.gwdg.de/~compbiol/foldseek

Noted thanks, will do for anything written up but for preliminary work it's helpful that the expensive computes for DALI and TMalign are included in the downloads for the foldseek...

Hi @martin-steinegger with `--format-output "query,target,evalue"` foldseek completes SCOP40 quickly but the sensitivity is lower than reported in the paper. Presumably I need to tweak some options such as `--max-seqs` and...

Much better! Seems accuracy is getting close to DALI now, is there any explanation of improvements in the algorithm?

hello @12047019 sorry I don't know -- this is a question for the foldseek authors, I couldn't figure out the exact version myself, I had to use the scop_lookup.fix.tsv file...

Update -- Rough estimate, looks like this compute would need1,000 vCPU-days which is over my budget. If you guys have pre-computed SCOP40 results or would like to run this, I'm...

As suggested by the warning message, these sequences are *much* too long, they are surely not suitable for global multiple alignment. R On Tue, Apr 16, 2024 at 1:26 PM...

Version 1 was the first commit to this repo. To make this easier for users to access, I added a branch `version1` and a release which has a pre-compiled linux...

FYI I consider palmscan obsolete, I would recommend using [https://github.com/rcedgar/palm_annot](https://github.com/rcedgar/palm_annot) which supports nt sequences and is much more sensitive than palmscan with much better FP rates.