This project will enhance the MASTERCATALOG, EraGen's product that combines an evolutionarily organized protein sequence database with tools to enable phylogenomics analysis. This will help maintain the commercial advantage of the MASTERCATALOG over public databases and tools, and help ensure that the MASTERCATALOG continues to enjoy its status as the "best in class" phylogenomic package. A key tactic in phylogenomic analysis correlates events in the genomic record with changing physiology of organisms, as recorded in the fossil and geological records. This correlation requires assignment of approximate dates to events in the genome record starting from sequence data (a "molecular clock"). The investigator and others at the Foundation for Applied Molecular Evolution have developed a tool (Transition Redundant Exchange, or TREx) that exploits silent substitutions to create a molecular clock that can be calibrated better than standard clocks, and can be used when transition rate constants and codon biases are not time-invariant in the lineages considered. A preliminary test of the TREx tool correlated events in the genomic and fossil records of several vertebrates, and estimated different transition rate constants in different vertebrate lineages. EraGen is therefore interested in incorporating this tool into the MASTERCATALOG. Phase I shall demonstrate the feasibility of doing this by calibrating the clock in many vertebrates, and demonstrating that rapid change at silent sites, which makes the clock problematic for dating the most distant divergences in vertebrates (fish-human), is overcome by reconstructing ancestral states. Reconstruction has enhanced other phylogenomics tools in the Foundation. If feasibility is shown, in Phase II, an EraGen-Foundation collaboration will develop software to generate TREx dates for nodes in the ca. 100,000 family trees in the MASTERCATALOG, creating an enhanced product that will have improved market value by providing better annotation.