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.
      Name                          Last modified      Size  Description
Parent Directory - chr1.gz 2006-07-20 16:12 35M chr1_random.gz 2006-07-20 16:12 53K chr2.gz 2006-07-20 16:12 28M chr2_random.gz 2006-07-20 16:13 22K chr3.gz 2006-07-20 16:13 22M chr4.gz 2006-07-20 16:13 19M chr4_random.gz 2006-07-20 16:13 47K chr5.gz 2006-07-20 16:13 13M chr5_random.gz 2006-07-20 16:13 12K chr6.gz 2006-07-20 16:13 7.4M chr6_random.gz 2006-07-20 16:13 2.5K chr7.gz 2006-07-20 16:13 9.7M chr7_random.gz 2006-07-20 16:13 38K chr8.gz 2006-07-20 16:14 7.9M chr8_random.gz 2006-07-20 16:14 148K chr9.gz 2006-07-20 16:14 5.5M chr10.gz 2006-07-20 16:12 6.0M chr10_random.gz 2006-07-20 16:12 2.1K chr11.gz 2006-07-20 16:12 5.9M chr11_random.gz 2006-07-20 16:12 5.3K chr12.gz 2006-07-20 16:12 4.7M chr12_random.gz 2006-07-20 15:44 0 chr13.gz 2006-07-20 16:12 4.1M chr13_random.gz 2006-07-20 16:12 8.3K chr14.gz 2006-07-20 16:12 4.2M chr15.gz 2006-07-20 16:12 3.6M chr16.gz 2006-07-20 16:12 196K chr16_random.gz 2006-07-20 16:12 64K chr17.gz 2006-07-20 16:12 3.2M chr18.gz 2006-07-20 16:12 3.1M chr18_random.gz 2006-07-20 16:12 11K chr19.gz 2006-07-20 16:12 3.1M chr20.gz 2006-07-20 16:12 3.6M chr20_random.gz 2006-07-20 16:12 20K chr21.gz 2006-07-20 16:12 2.3M chr22.gz 2006-07-20 16:12 1.1M chr22_random.gz 2006-07-20 16:12 36K chr23.gz 2006-07-20 16:13 1.6M chr24.gz 2006-07-20 16:13 2.0M chr25.gz 2006-07-20 16:13 553K chr25_random.gz 2006-07-20 16:13 8.8K chr26.gz 2006-07-20 16:13 1.7M chr27.gz 2006-07-20 16:13 1.3M chr28.gz 2006-07-20 16:13 1.4M chr28_random.gz 2006-07-20 16:13 49K chrE22C19W28_E50C23.gz 2006-07-20 16:14 399K chrE22C19W28_E50C23_random.gz 2006-07-20 16:14 80K chrE64.gz 2006-07-20 16:14 29K chrE64_random.gz 2006-07-20 16:14 100K chrM.gz 2006-07-20 16:14 22K chrUn_random.gz 2006-07-20 16:14 14M chrW.gz 2006-07-20 16:14 35K chrW_random.gz 2006-07-20 16:14 148K chrZ.gz 2006-07-20 16:14 13M chrZ_random.gz 2006-07-20 16:14 75K md5sum.txt 2006-07-20 16:34 2.5K