This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/monDom5/phastCons9way/README.txt

This directory contains compressed phastCons scores for multiple
alignments of 9 vertebrate genomes to the opossum genome.

Files in this directory are:
    ave.cons.mod
    ave.noncons.mod              phastCons tree models with branch lengths
                                 for all nine species

    wig/chr*.wig.gz              per-chromosome phastCons scores for all 9 
                                 species

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/monDom5/multiz9way/

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

Assemblies used in these alignments:

    _ Opossum         Monodelphis domestica          Oct. 2006   monDom5
    _ Wallaby         Macropus eugenii               Nov. 2007   macEug1
    _ Human           Homo sapiens                   Mar. 2006   hg18
    _ Mouse           Mus musculus                   July 2007   mm9
    _ Dog             Canis lupus familiaris         May  2005   canFam2
    _ Platypus        Ornithorhynchus anatinus       Mar. 2007   ornAna1
    _ Chicken         Gallus gallus                  May  2006   galGal3
    _ X. tropicalis   Xenopus tropicalis             Aug. 2005   xenTro2
    _ Zebrafish       Danio rerio                    July 2007   danRer5

---------------------------------------------------------------
To download a large file or multiple files from this directory, we recommend 
that you use rsync or ftp rather than downloading the files via our website.
There is approximately 3.8 Gb of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/monDom5/phastCons9way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/monDom5/phastCons9way

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.

---------------------------------------------------------------
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.

---------------------------------------------------------------
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                                                       -   
      ave.cons.mod                                      2009-02-23 00:08  530   
      ave.noncons.mod                                   2009-02-23 00:09  530   
      wig/                                              2009-09-29 14:29    -