PAINT is a java application for viewing tree files. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
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Brief Bioinform. 2011 Sep;12(5):449-62. Epub 2011 Aug 27.
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.
Gaudet P, Livstone MS, Lewis SE, Thomas PD.