This directory contains compressed phastCons scores for multiple
alignments of the following assemblies to the Mouse May 2004 (mm5) 
genome: 
  - Rat Jun. 2003 (rn3) 
  - Human May 2004 (hg17)
  - Dog Jul. 2004 (canFam1)
  - Chicken Feb. 2004 (galGal2) 

Each mouse chromosome has a corresponding data file. When uncompressed, 
the data file contains two columns: a one-based coordinate and a score 
showing the posterior probability that phastCons's phylogenetic hidden 
Markov model (HMM) is in its most-conserved state at that base position.

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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/mm5/phastCons/mzRn3Hg17Cf1Gg2/. To download 
multiple files, use the "mget" command:

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

All the tables in this directory are freely usable for any 
purpose.  For data use restrictions regarding the dog and chicken genomes, 
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 Conservation track in the Genome
Browser.
      Name                       Last modified      Size  Description
Parent Directory - chr1.gz 2004-10-11 11:26 631M chr1_random.gz 2004-10-11 12:34 3.2M chr2.gz 2004-10-11 11:36 630M chr2_random.gz 2004-10-11 12:35 21M chr3.gz 2004-10-11 11:43 507M chr3_random.gz 2004-10-11 12:35 5.6M chr4.gz 2004-10-11 11:51 505M chr4_random.gz 2004-10-11 12:35 22M chr5.gz 2004-10-11 11:59 487M chr5_random.gz 2004-10-11 12:35 6.0M chr6.gz 2004-10-11 12:07 488M chr6_random.gz 2004-10-11 12:35 3.6M chr7.gz 2004-10-11 12:13 427M chr7_random.gz 2004-10-11 12:36 17M chr8.gz 2004-10-11 12:20 423M chr8_random.gz 2004-10-11 12:36 3.3M chr9.gz 2004-10-11 12:26 419M chr9_random.gz 2004-10-11 12:36 1.5M chr10.gz 2004-10-11 12:43 422M chr10_random.gz 2004-10-11 13:30 1.0M chr11.gz 2004-10-11 12:49 428M chr12.gz 2004-10-11 12:55 379M chr12_random.gz 2004-10-11 13:30 4.8M chr13.gz 2004-10-11 13:01 375M chr13_random.gz 2004-10-11 13:30 4.1M chr14.gz 2004-10-11 13:07 379M chr14_random.gz 2004-10-11 13:30 4.6M chr15.gz 2004-10-11 13:12 340M chr15_random.gz 2004-10-11 13:30 1.4M chr16.gz 2004-10-11 13:18 320M chr16_random.gz 2004-10-11 13:30 2.9M chr17.gz 2004-10-11 13:22 291M chr17_random.gz 2004-10-11 13:30 2.5M chr18.gz 2004-10-11 13:27 297M chr18_random.gz 2004-10-11 13:30 3.0M chr19.gz 2004-10-11 13:30 203M chr19_random.gz 2004-10-11 13:30 1.4M chrM.gz 2004-10-11 12:26 54K chrUn_random.gz 2004-10-11 13:33 126M chrX.gz 2004-10-11 12:33 428M chrX_random.gz 2004-10-11 12:36 18M chrY.gz 2004-10-11 12:34 75M chrY_random.gz 2004-10-11 12:36 738K md5sum.txt 2004-10-11 14:03 1.9K