Benjamin Buchfink
Benjamin Buchfink
Sorry, I didn't have time yet to look into it again. It could still take some time until I provide a fix.
The issue should be fixed in v2.1.1, at least it is working correctly now for the example you sent me. I'm not sure what the problem was, but the affected...
The rows are always grouped by query.
I'm sure there's tools out there that can do this but I'm not the right person to ask, maybe a website like https://www.biostars.org/ can help you.
`cluster` uses a default id% cutoff of 50% and `deepclust` of 0%, that is the only difference between the two. `linclust` uses a default cutoff of 90% and only runs...
> Can I use diamond deepclust to cluster orthologs and get ortholog families like OrthoMCL or orthofinder2 ? Some people use it like that and with the right cutoff settings...
It could be that the proteins of these species for some reason attract more hits than those of the other species, without seeing the data I can't really answer this.
If the sequences are mostly identical the algorithm will always pick the ones that come first in the input file as representatives. So yes in that case you would expect...
This should be fixed in the latest release.
Hits are not sorted by score but by evalue, as you can see the first hit has a lower evalue despite its lower score. That happens sometimes since the target...