Using OrthoMCL on command line

Question

[DNAlias]

I want to use the OrthoMCL clustering algorithm to create clusters within a set of some genes that I have from several species. I don't need to connect these to any existing clusters, I just want to see how these genes connect to each other in a vacuum. Is there a way that I can use the OrthoMCL website to do this? If not, is there a way to use OrthoMCL to do this without using MySQL?

Answer 1

[dariober]

Unless you really need/want to use OrthoMCL, use orthofinder instead. It should give the same type of output as OrthoMCL but orthofinder is generally more accurate, maintained, and easier to install.