This directory contains compressed phastCons scores for multiple
alignments of 5 other nematode genomes to the C. elegans genome:

  - C. elegans      May 2008, ce6          reference
  - C. remanei      May 2007, caeRem3      chain net
  - C. briggsae     Jan 2007, cb3          chain net
  - C. brenneri     Feb 2008, caePb1       chain net
  - C. japonica     Mar 2008, caeJap1      chain net
  - P. pacificus    May 2007, priPac1      chain net

Files in this directory are:
    6way.conserved.mod      phastCons conserved tree model 
    6way.non-conserved.mod  phastCons non-conserved tree model
    chr*.data.gz - phastCons scores for the 6 species
    md5sum.txt - MD5 check sums for the *.data.gz and *.mod files

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/ce6/multiz6way/

For a description of the phastCons file format, see
http://genome.ucsc.edu/goldenPath/help/phastCons.html.

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To download a large file or multiple files from this directory, we recommend 
that you use ftp rather than downloading the files via our website. To do so: 
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/ce6/phastCons6way

To download multiple files from the UNIX command line, use the "mget" command. 
    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
Use the "prompt" command to toggle the interactive mode if you do not want 
to be prompted for each file that you download.

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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).

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      md5sum.txt              2008-06-23 14:59  443   
      chrX.data.gz            2008-06-18 12:00   18M  
      chrV.data.gz            2008-06-18 12:00   20M  
      chrM.data.gz            2008-06-18 12:00   18K  
      chrIV.data.gz           2008-06-18 12:00   15M  
      chrIII.data.gz          2008-06-18 12:00   13M  
      chrII.data.gz           2008-06-18 12:00   14M  
      chrI.data.gz            2008-06-18 11:59   14M  
      6way.non-conserved.mod  2008-06-18 11:40  444   
      6way.conserved.mod      2008-06-18 11:40  444