Gene clustering with OrthoMCL

Question

[Ric]

Hi, I would like to run OrthoMCL and as input, it requires protein sequences from desired organisms. Does OrthoMCL use assembled transcript from RNA-Seq?

Thank you in advance,

[Joe]

OrthoMCL is an orthologue clustering tool for defining core genomes/pangenomes etc. In theory you could use it with CDSs extracted from assembled transcripts, but I don't really see why you would do this (unless I'm missing something).

What are you trying to achieve?

[Juke34]

You should use cd-hit then.