This is a customized version of OrthoMCL based on v2.0.9 and which is used within the OrthoMCL Pipeline. To download please run.
$ git clone https://github.com/apetkau/orthomclsoftware-custom.git
To install please follow the instructions in the UserGuide.txt and other files within the doc/OrthoMCLEngine/Main/ directory.