This directory contains compressed phastCons scores for multiple
alignments of the following assemblies to the zebrafish genome
(danRer4, Mar. 2006):

 - Fugu (fr1, Aug. 2002)
 - Tetraodon (tetNig1, Feb. 2004)
 - X. tropicalis (xenTro2, Aug. 2005)
 - Opossum (monDom4, Jan. 2006)
 - Mouse (mm8, Feb. 2006)
 - Human (hg18, Mar. 2006)

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/danRer4/phastCons7wayScores. 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., 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 danRer3 Conservation track in the Genome
Browser.
      Name                    Last modified      Size  Description
Parent Directory - md5sum.txt 2006-05-30 09:27 1.2K chrUn_random.gz 2006-05-30 09:14 13M chrNA_random.gz 2006-05-30 09:14 49M chrM.gz 2006-05-30 09:13 26K chr9.gz 2006-05-30 09:13 13M chr8.gz 2006-05-30 09:13 15M chr7.gz 2006-05-30 09:13 19M chr6.gz 2006-05-30 09:13 16M chr5.gz 2006-05-30 09:13 18M chr4.gz 2006-05-30 09:12 11M chr3.gz 2006-05-30 09:12 16M chr25.gz 2006-05-30 09:12 9.2M chr24.gz 2006-05-30 09:12 10M chr23.gz 2006-05-30 09:12 12M chr22.gz 2006-05-30 09:12 11M chr21.gz 2006-05-30 09:12 12M chr20.gz 2006-05-30 09:11 14M chr2.gz 2006-05-30 09:11 15M chr19.gz 2006-05-30 09:11 11M chr18.gz 2006-05-30 09:11 12M chr17.gz 2006-05-30 09:11 14M chr16.gz 2006-05-30 09:11 14M chr15.gz 2006-05-30 09:10 13M chr14.gz 2006-05-30 09:10 21M chr13.gz 2006-05-30 09:10 14M chr12.gz 2006-05-30 09:10 13M chr11.gz 2006-05-30 09:10 11M chr10.gz 2006-05-30 09:09 12M chr1.gz 2006-05-30 09:09 16M