This directory contains compressed phastCons scores for multiple
alignments of the following assemblies to the zebrafish genome
(danRer2, Jun. 2004):

 - Human (hg17, May 2004)
 - Mouse (mm6, Mar. 2005)
 - Opossum (monDom1, Oct. 2004)
 - Fugu (fr1, Aug. 2002)
 - Tetraodon (tetNig1, Feb. 2004)

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/danRer2/phastCons6wayScores. To download 
multiple files, use the "mget" command:

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

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

A manuscript on phastCons is in preparation.

For a discussion of the methods used to calculate the phastCons scores,
see the description page for the danRer2 Conservation track in the Genome
Browser.
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