Calculating Phastcons And Phylop Scores

Question

[anuragm]

I want to know how exactly the conservation scores are calculated. I looked up this site but all I get is a rough idea. Could anyone provide me links/material that deals with the mathematical treatment of conservation scores - especially PhastCons and PhyloP

Thanks!

[Asaf]

On the left you have links to PhastCons and PhyloP manuals, at the end of each manual there is a list of relevant literature

Answer 1

[Ian]

If you go to the conservation track in the UCSC browser (http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=193841314&c=chr21&g=cons46way) the key publication for phastCons appears to be Siepel et al. 2005. Apart from that I cannot find anything else.