This directory contains compressed phastCons scores for multiple
alignments of the following assemblies to the rat genome
(Nov. 2004, rn4):

  - mouse (Feb 2006, mm8)
  - human (Mar 2006, hg18) 
  - dog (May 2005, canFam2) 
  - cow (Mar 2005, bosTau2) 
  - opossum (Jan 2006, monDom4) 
  - chicken (Feb 2004, galGal2) 
  - frog (Oct 2004, xenTro1) 
  - zebrafish (May 2005, danRer3) 

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/rn4/phastCons9way. 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 - md5sum.txt 2006-04-03 10:41 2.0K chrX_random.gz 2006-04-03 10:38 423K chrX.gz 2006-04-03 10:38 76M chrUn_random.gz 2006-04-03 10:37 2.1M chrUn.gz 2006-04-03 10:37 21M chrM.gz 2006-04-03 10:37 16K chr20_random.gz 2006-04-03 10:30 249K chr20.gz 2006-04-03 10:30 28M chr19_random.gz 2006-04-03 10:28 478K chr19.gz 2006-04-03 10:28 32M chr18_random.gz 2006-04-03 10:28 214K chr18.gz 2006-04-03 10:28 47M chr17_random.gz 2006-04-03 10:28 190K chr17.gz 2006-04-03 10:28 50M chr16_random.gz 2006-04-03 10:27 519K chr16.gz 2006-04-03 10:27 46M chr15_random.gz 2006-04-03 10:26 691K chr15.gz 2006-04-03 10:26 56M chr14_random.gz 2006-04-03 10:26 724K chr14.gz 2006-04-03 10:26 57M chr13_random.gz 2006-04-03 10:25 164K chr13.gz 2006-04-03 10:25 54M chr12_random.gz 2006-04-03 10:25 291K chr12.gz 2006-04-03 10:24 23M chr11_random.gz 2006-04-03 10:24 542K chr11.gz 2006-04-03 10:24 48M chr10_random.gz 2006-04-03 10:24 414K chr10.gz 2006-04-03 10:24 63M chr9_random.gz 2006-04-03 10:37 532K chr9.gz 2006-04-03 10:37 63M chr8_random.gz 2006-04-03 10:36 358K chr8.gz 2006-04-03 10:36 72M chr7_random.gz 2006-04-03 10:35 475K chr7.gz 2006-04-03 10:35 76M chr6_random.gz 2006-04-03 10:34 744K chr6.gz 2006-04-03 10:34 79M chr5_random.gz 2006-04-03 10:33 828K chr5.gz 2006-04-03 10:33 88M chr4_random.gz 2006-04-03 10:32 792K chr4.gz 2006-04-03 10:32 98M chr3_random.gz 2006-04-03 10:31 772K chr3.gz 2006-04-03 10:31 95M chr2_random.gz 2006-04-03 10:30 1.7M chr2.gz 2006-04-03 10:30 132M chr1_random.gz 2006-04-03 10:23 1.4M chr1.gz 2006-04-03 10:23 137M