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 chr2.gz 2004-10-11 11:36 630M chr3.gz 2004-10-11 11:43 507M chr4.gz 2004-10-11 11:51 505M chr6.gz 2004-10-11 12:07 488M chr5.gz 2004-10-11 11:59 487M chrX.gz 2004-10-11 12:33 428M chr11.gz 2004-10-11 12:49 428M chr7.gz 2004-10-11 12:13 427M chr8.gz 2004-10-11 12:20 423M chr10.gz 2004-10-11 12:43 422M chr9.gz 2004-10-11 12:26 419M chr12.gz 2004-10-11 12:55 379M chr14.gz 2004-10-11 13:07 379M chr13.gz 2004-10-11 13:01 375M chr15.gz 2004-10-11 13:12 340M chr16.gz 2004-10-11 13:18 320M chr18.gz 2004-10-11 13:27 297M chr17.gz 2004-10-11 13:22 291M chr19.gz 2004-10-11 13:30 203M chrUn_random.gz 2004-10-11 13:33 126M chrY.gz 2004-10-11 12:34 75M chr4_random.gz 2004-10-11 12:35 22M chr2_random.gz 2004-10-11 12:35 21M chrX_random.gz 2004-10-11 12:36 18M chr7_random.gz 2004-10-11 12:36 17M chr5_random.gz 2004-10-11 12:35 6.0M chr3_random.gz 2004-10-11 12:35 5.6M chr12_random.gz 2004-10-11 13:30 4.8M chr14_random.gz 2004-10-11 13:30 4.6M chr13_random.gz 2004-10-11 13:30 4.1M chr6_random.gz 2004-10-11 12:35 3.6M chr8_random.gz 2004-10-11 12:36 3.3M chr1_random.gz 2004-10-11 12:34 3.2M chr18_random.gz 2004-10-11 13:30 3.0M chr16_random.gz 2004-10-11 13:30 2.9M chr17_random.gz 2004-10-11 13:30 2.5M chr9_random.gz 2004-10-11 12:36 1.5M chr15_random.gz 2004-10-11 13:30 1.4M chr19_random.gz 2004-10-11 13:30 1.4M chr10_random.gz 2004-10-11 13:30 1.0M chrY_random.gz 2004-10-11 12:36 738K chrM.gz 2004-10-11 12:26 54K md5sum.txt 2004-10-11 14:03 1.9K