This directory contains compressed phastCons scores for multiple
alignments of the following assemblies to the C. elegans genome
(ce4, WS170, Jan. 2007):

  - C. brenneri (Jan. 2007, caePb1)
  - C. remanei (Mar. 2006, caeRem2)
  - C. briggsae (Jan. 2007, cb3)
  - P. pacificus (Feb. 2007, priPac1) 

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/ce4/phastCons5wayScores. 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 ce4 Conservation track in the Genome
Browser.

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      chrM.data.gz            2007-05-03 15:26   18K  
      chrIII.data.gz          2007-05-03 15:26   15M  
      chrI.data.gz            2007-05-03 15:25   15M  
      chrII.data.gz           2007-05-03 15:26   16M  
      chrIV.data.gz           2007-05-03 15:26   17M  
      chrX.data.gz            2007-05-03 15:27   19M  
      chrV.data.gz            2007-05-03 15:26   22M