PANTHER trees aim to accurately represent ‘all’ of the evolutionary events in the gene family; for PANTHER 7, this means accurately inferring speciation and gene duplication events. For the gene trees, we use a novel algorithm, GIGA (Gene tree Inference in the Genomic Age). GIGA makes use of the known species tree and the presumably complete gene sets to infer accurate gene trees and locate gene duplication events relative to speciation events. If more than one gene duplication event took place between given consecutive speciation events, this appears as a single, multifurcating duplication node (e.g. node ‘2’ in Figure 2). The algorithm also performs a fast, approximate reconstruction of ancestral protein sequences at each node in the tree, using an iterative procedure starting at the leaves of the tree (modern day sequences) that considers the descendant sequences and the nearest outgroup.
