This directory contains compressed phastCons scores for multiple
alignments of 28 vertebrate genomes to the human genome,
plus an alternate set of scores for the placental mammal
subset of species in the alignments.  

Files in this directory are:
    28way.mod           phastCons tree model with branch lengths
                           for all 28 species
    placental.mod       phastCons tree model for the placental subset
    vertebrate/*.pp.gz  phastCons scores for 28 species
    placental/*.pp.gz   phastCons scores for placental subset (18 species)

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way

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/hg18/phastCons28way

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                             -   
      28way.mod               2007-05-06 10:36  1.0K  
      placental.mod           2007-05-09 11:47  778   
      placental/              2007-06-05 17:14    -   
      vertebrate/             2007-06-05 17:14    -