This directory contains compressed phastCons scores for multiple
alignments of the following assemblies to the chicken genome
(May 2006, galGal3):

  - human (Mar 2006, hg18) 
  - mouse (Feb 2006, mm8)
  - rat (Nov. 2004, rn4)
  - opossum (Jan 2006, monDom4) 
  - X. tropicalis (Aug. 2005, xenTro2)
  - zebrafish (Mar 2006, danRer4) 

For a description of the phastCons file format, see
http://genome.ucsc.edu/goldenPath/help/phastCons.html.

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If you plan to download a large file or multiple files from this 
directory, we recommend you use ftp rather than downloading the files 
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to 
the directory goldenPath/galGal3/phastCons7way. To download multiple files, 
use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)

All files in this directory are freely available for public use.
For data use restrictions regarding the other genome assemblies used 
in this annotation, see http://genome.ucsc.edu/goldenPath/credits.html.

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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 Statistical Methods in Molecular Evolution (ed. Nielsen, R.) (Springer,
2005). 

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