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?
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).
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?
You should use cd-hit then.