This directory contains compressed phastCons scores for multiple
alignments of the following assemblies to the Mouse May 2004 (mm5) 
genome: 
  - Rat Jun. 2003 (rn3) 
  - Human May 2004 (hg17)
  - Dog Jul. 2004 (canFam1)
  - Chicken Feb. 2004 (galGal2) 

Each mouse chromosome has a corresponding data file. When uncompressed, 
the data file contains two columns: a one-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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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/mm5/phastCons/mzRn3Hg17Cf1Gg2/. To download 
multiple files, use the "mget" command:

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

All the tables in this directory are freely usable for any 
purpose.  For data use restrictions regarding the dog and chicken genomes, 
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 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.
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