(29), generates accurate ancestral sequences across each region. Ortheus uses a branch transducer model, a type of HMM, to call deletion and insertion events, providing a realistic model under which it can infer the ancestral sequence. Figure 2 shows the results of GERP (30) analysis of constraint across different feature types found in Ensembl, showing a sharp distinction between coding exons and ancestral repeats, with regulatory regions showing a intermediate level of constraint. Ensembl release 49 (March 2008) saw the first set of EPO alignments on a set of seven mammals. In release 50 (July 2008), this set of alignments was extended to include low-coverage genomes, creating a 23 mammals EPO alignment. A set of 4-way primate EPO alignments was also added containing human, chimp, orangutan, macaque. We plan to produce EPO multiple alignments in the teleost lineage in the future.
