Both phastCons (25) and phyloP (26) conservation scores have been computed separately for three groups of organisms: 8 primates alone, 31 placental mammals, and all 44 vertebrates. The two conservation scores are informative in different ways. The phastCons score takes neighboring bases into account, estimating the probability that each nucleotide belongs to a conserved element. It is sensitive to ‘runs’ of conserved sites and is used to create the Conserved Elements subtrack of the Conservation track. The phyloP score is a separate measurement of conservation at each base, ignoring neighboring bases in its calculation. It can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). PhyloP is useful for evaluating signatures of selection at particular nucleotides (e.g. third codon positions, or first positions of miRNA target sites). Figure 1 shows a subset of species in the 44-way multiple alignment track and all six conservation score tracks.
