This directory contains compressed phastCons scores for multiple
alignments of 4 other vertebrate genomes to the cow genome:

  - cow             Bos taurus              Oct 2007, bosTau4  reference
  - dog             Canis familiaris        May 2005, canFam2  syntenic net
  - human           Homo sapiens            Mar 2006, hg18     syntenic net
  - mouse           Mus musculus            July 2007, mm9     syntenic net
  - platypus        Ornithorhychus anatinus Mar 2007, ornAna1  syntenic net

Files in this directory are:
    5way.mod      phastCons tree model with branch lengths for the 5 species
    file_*.data.gz - phastCons scores for the 5 species
	each file contains the data for a number of chromosomes or
	the chrUn contigs for the Cow genome

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/multiz5way/

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

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To download a large file or multiple files from this directory, we recommend 
that you use ftp rather than downloading the files via our website. To do so: 
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/bosTau4/phastCons5way

To download multiple files from the UNIX command line, use the "mget" command. 
    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
Use the "prompt" command to toggle the interactive mode if you do not want 
to be prompted for each file that you download.

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All the files in this directory are freely available for public use.
For data use restrictions regarding the 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 R. Nielsen, ed., Statistical Methods in Molecular Evolution,
Springer (in press) (2004).