Phylop Conservation Score Based On Human, Chimp, Orangutan And Rhesus Genomes

Question

[New2R]

How can one generate PhyloP values for only a few species (entire genome) ...say Human, Chimp, Orangutan and Rhesus...instead of relying on the PhyloP values for 44 or 46 species (that includes Primate, placental mammals, and vertebrates species) that can be downloaded from UCSC website? This is because genome sequences of some species are bad and including them in the PhyloP calculation could lead to bias. I am assuming that this would involve using PHAST. It would be helpful to know the detailed scripts to use as I am new to scripting environment. or are there other ways? Thanks in advance.

[Manvendra Singh]

There are some 11way 46 way conservation table there on UCSC