PANTHER version 19.0 contains 15683 protein families, each with a phylogenetic tree relating modern-day genes in 144 organisms.

Phylogenetic trees also infer the evolutionary events that occurred, namely speciation (green nodes) and gene duplication events (orange nodes). Horizontal transfer events are not inferred in this version of PANTHER, but will appear in future versions.

Expert biologists have divided each family into subfamilies, which are generally orthologous groups but may also contain recently duplicated paralogs. Each family and subfamily is also represented as a hidden Markov model (HMM), which can be used to classify new sequences to an existing subfamily.