This directory contains compressed phastCons scores for multiple
alignments of the following assemblies to the Human Jul. 2003 (hg16)
genome:
 - Chimp Nov. 2003 (panTro1)
 - Mouse Feb 2003 (mm3)
 - Rat Jun. 2003 (rn3)
 - Chicken Feb. 2004 (galGal2) 

Each human chromosome has a corresponding data file. When uncompressed, 
the data file contains two columns: a 1-based coordinate and a score 
showing the posterior probability that phastCons's phylogenetic hidden 
Markov model (HMM) is in its most-conserved state at that base position.

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References for phastCons:

Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., 
Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., 
Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W., 
and Haussler, D.  Evolutionarily conserved elements in vertebrate, insect, 
worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
(http://www.genome.org/cgi/doi/10.1101/gr.3715005)

Siepel, A. and Haussler, D. Phylogenetic hidden Markov models. 
In R. Nielsen, ed., Statistical Methods in Molecular Evolution,
Springer (in press) (2004).

For a discussion of the methods used to calculate the phastCons scores,
see the description page for the Conservation track in the Genome
Browser.