Which directories for versions of Orthofinder v2.4.0 (or more recent) are valid with the HOGs?

[SheepwormJM]

Hi,

Thank you for this really useful tool.

I am looking for information as to which of the output directories are not deprecated. I understand from the github readme page that the Orthogroups directory is deprecated. However, from some of the comments it looks like the stats in another directory also relate to the older Orthogroups, and not the Phylogenetic_Hierarchical_Orthogroups.

Please could you help me know which directories will contain data related to the new Phylogenetic_Hierarchical method? Are the orthologues in the Orthologues directory identified by the same method for example? Or are these related to the older Orthogroups data?

Thanks, Jenni