OMA Groups are sets of genes which are all orthologous to each other according to the definition of Fitch (1970). In presence of a duplication in certain gene familly, this grouping strategy will pick only one of the two lineages resulting from the duplication event. The hierarchical orthologous groups (HOGs) are defined as sets of genes that have descended from a single common ancestor within a taxonomic range of interest, i.e. they correspond to the member of a clade in a gene tree rooted at the speciation node of interest. Which type of groups you should choose depends highly on the type of your analysis.

For the OMA Groups, we apply a very stringent grouping strategy. All the members of a group need to be bona fide orthologs to each other, i.e. the form a clique in graph-theoretic terms. This grouping strategy is mainly intended for applications which require orthologs of high confidence, e.g. for reconstructing species trees. A gene tree built from the members of an OMA Group should - in absence of LGT are incomplete lineage sorting - be congruent with the underlying species tree. If you are interested in larger groups, consider using the OMA HOGs. These hierarchical orthologous groups are defined as set of genes that all started diverging from a single ancestral gene at a given time point of reference.

The OMA Browser is available under the Creative Commons Attribution-Share Alike 2.5 License, and the OMA standalone package under the MPL 2.0 (open source) licence.