PGA: A Program for Genome Annotation by Comparative Analysis of Maximum   Likelihood Phylogenies of Genes and Species
  The Phylogenetic Genome Annotator (PGA) is a computer program that enables real-time comparison of 'gene trees' versus 'species trees' obtained from predicted open reading frames of whole genome data. The gene phylogenies are inferred for each individual genome predicted proteins whereas the species phylogenies are inferred from rDNA data. The correlated protein domains, defined by PFAM, are then displayed side-by-side with a phylogeny of the corresponding species. The statistical support of gene clusters (branches) is given by the quartet puzzling method. This analysis readily discriminates paralogs from orthologs, enabling the identification of proteins originated by gene duplications and the prediction of possible functional divergence in groups of similar sequences. 
Paulo Bandiera-Paiva and Marcelo R.S. Briones
q-bio.PE q-bio.GN