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".