Conservation scores and constrained elements
We use GERP to calculate conservation scores and call constrained elements on the amniota vertebrate Pecan, mammals EPO_LOW_COVERAGE, fish EPO_LOW_COVERAGE and sauropsids EPO_LOW_COVERAGE multiple alignments. Calculation of these scores for different species groups allows the determination of regions that are conserved in one taxon but not another.
Conservation scores are calculated per base, indicating how many species in a given multiple alignment match at each locus.
Constrained elements are stretches of the multiple alignment where the sequences are highly conserved according to the previous score. This is done using GERP, which uses a permutation test to identify specific segments of the alignment that appear to be more conserved than expected by random chance.