This might be a very trivial question to ask .. I have been using conservation track data from UCSC for sometime now.. I wanted to know how exactly are different types of conservation scores calculated ? I'd read somewhere that PhyloP looks at individual nucleotide positions while PhastCons takes into account adjacent regions as well and hence, it makes more sense to look at Phast for conservation. If someone knows of some useful papers/links that explain this matter it would be of great help.