a multiple sequence alignment (MSA) (Figure 1). Protein family trees are constructed computationally from sequence data using a phylogenetic tree inference algorithm called GIGA24. Nodes in the tree, corresponding to common ancestors of extant family members, are annotated by expert biologists with their inferred GO terms and PANTHER protein class terms, based on experiments performed on extant proteins. Subfamilies are determined based on the tree structure and often define the orthologous group, especially in organisms in the Deuterostomia superphylum. The functional annotations are propagated from the annotated ancestral nodes to the subfamily nodes, each of which is also represented by an HMM to allow classification of newly discovered protein sequences (Figure 2A). In addition, the HMM library and the scoring pipeline allow users to analyze genome-wide data from any organisms outside of the 82 within the PANTHER system (see below). Phylogenetic tree and functional annotation at the ancestral nodes have great advantage in annotation of previously unclassified genes. The PANTHER phylogenetic trees are currently used by the Gene Ontology Consortium in its curation pipeline 22.
