Pyham (Python HOG Analysis Method): slicing hierarchical orthologous groups stored in OrthoXML files

OMA Standalone can produce an OrthoXML output file containing all hierarchical orthologous groups. To facilitate analysis of HOGs such as

• identifying lineage-specific HOGs
• keeping track of gains and losses across taxonomic ranges
• count the number of HOGs inferred for a particular taxonomic level

we have developed a Python tool called pyham (Python HOG Analysis Method), also previously known as "Family Analyzer".

Links

• Code: Git repo
• Documentation: Installation, basics API
• Tutorial: general usage