The exoniphy program identifies evolutionarily conserved protein-coding exons in multiple, aligned sequences using a phylogenetic hidden Markov model (phylo-HMM), a kind of statistical model that simultaneously describes exon structure and exon evolution. This track shows exoniphy predictions for the human Jul. 2003 (hg16), mouse Feb. 2003 (mm3), and rat Jun. 2003 (rn3) genomes, as aligned by the multiz program.
Exoniphy is described in Siepel A & Haussler D (2004), "Computational identification of evolutionarily conserved exons," RECOMB '04. Multiz is described in Blanchette M et al. (2004), "Aligning multiple genomic sequences with the threaded blockset aligner," Genome Res. 14:708-175.