GETHOGs is a library to infer hierarchical orthologous groups from pairwise evolutionary relationship and its related reference species tree. Infered HOGs are provided as orthoXML ( see http://orthoxml.org.). GETHOGs can be used as a python library or using the CLI script in the bin folder.
For extended documentation, please check the related paper "Clément-Marie Train, Natasha M. Glover, Gaston H. Gonnet, Adrian M. Altenhoff, Christophe Dessimoz; Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference, Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages i75–i82, https://doi.org/10.1093/bioinformatics/btx229" or look at the docs folder that contain information on common use cases and API documentation of the library.
GETHOGs is written in python3.
Consider using pip to install the package directly from a checked out git repo
python -m pip install --upgrade pip
pip install gethogs