This directory contains compressed phastCons scores for multiple
alignments of 30 vertebrate genomes to the mouse genome,
plus an alternate set of scores for the euchontoglires
subset of species in the alignments,  
and an alternate set of scores for the placental mammal
subset of species in the alignments.  

Files in this directory are:
    vertebrate.mod      phastCons tree model with branch lengths
                           for all 30 species
    euarchontoglires.mod phastCons tree model for the euarchontoglires subset
    placental.mod        phastCons tree model for the placental subset
    vertebrate/*.data.gz phastCons scores for 30 species
    euarchontoglires/*.data.gz  phastCons scores for placental subset (11 species)
    placental/*.data.gz  phastCons scores for placental subset (20 species)

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/mm9/multiz30way/

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/mm9/phastCons30way

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                             -   
      vertebrate.mod          2007-10-22 16:42  1.1K  
      placental.mod           2007-10-31 12:33  834   
      euarchontoglires.mod    2007-10-31 10:30  582   
      vertebrate/             2007-11-05 10:44    -   
      placental/              2007-11-05 10:44    -   
      euarchontoglires/       2007-11-05 10:45    -