PANTHER (Protein ANalysis THrough Evolutionary Relationships) is a database of phylogenetic trees of protein-coding gene families from all kingdoms of life (1). Ancestral genes (representing most recent common ancestors of extant genes) are annotated with ontology terms describing gene function, and likely functional divergence events are identified and used to divide protein families into subfamilies of genes with similar function. Hidden Markov models (HMMs) are constructed for all families and subfamilies, which can be used for genome annotation projects, alone or as part of the InterPro database (2) that includes PANTHER as well as several other well-known protein annotation resources.
