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.
Thanks
2 answers
There's some references at UCSC.
Background (and references) in addition to Comparison with other packages and Frequently asked questions on the PHAST website. This Biostars post may shed some light too.
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