I am super happy I discovered this parallel much faster version. However, I find that sometimes orthoMCL performs better or is at least more stable. I typically work with clustering orthologs of very similar sequences like strains of viruses or human primate sequences - so it could be that this small differences between sequences is causing issues.
Essentially I am at times seeing less clusters than what orthoMCL would produce. Today I was clustering Monkeypox ORFs, and while orthoMCL assigned a cluster for all 186 ORFs of my reference genome ORFs, porthoMCL only assigned 36 ORFs to clusters. It's bizzare because it classified correctly all the ORFs of the other similar 11 viruses.
I am also frequently noticing that one taxa will have 0's for all pairwise comparisons in 6.ortholog file. There isn't an obvious reason. Yesterday it was one primate organism out of 15 and today it was a virus out of 11. Rerunning all the steps does not seem to fix the issue.
How are blast scores normalized for mclInput? Thanks
I am super happy I discovered this parallel much faster version. However, I find that sometimes orthoMCL performs better or is at least more stable. I typically work with clustering orthologs of very similar sequences like strains of viruses or human primate sequences - so it could be that this small differences between sequences is causing issues.
Essentially I am at times seeing less clusters than what orthoMCL would produce. Today I was clustering Monkeypox ORFs, and while orthoMCL assigned a cluster for all 186 ORFs of my reference genome ORFs, porthoMCL only assigned 36 ORFs to clusters. It's bizzare because it classified correctly all the ORFs of the other similar 11 viruses.
I am also frequently noticing that one taxa will have 0's for all pairwise comparisons in 6.ortholog file. There isn't an obvious reason. Yesterday it was one primate organism out of 15 and today it was a virus out of 11. Rerunning all the steps does not seem to fix the issue.
How are blast scores normalized for mclInput? Thanks