This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/felCat4/phastCons6way/README.txt


This directory contains compressed phastCons scores for multiple alignments
of 5 mammal genomes to the cat genome. Assemblies used in these alignments:


  - Cat             Felis catus             Dec 2008 felCat4  reference
  - Dog             Canis lupus familiaris  May 2005 canFam2  chain net
  - Panda           Ailuropoda melanoleuca  Dec 2009 ailMel1  recip best
  - Human           Homo sapiens            Feb 2009 hg19     chain net
  - Mouse           Mus musculus            Jul 2007 mm9      chain net
  - Opossum         Monodelphis domestica   Oct 2006 monDom5  chain net

Files in this directory are:
    all.mod      phastCons tree model with branch lengths
                 for all 6 species

    phastCons6way.wigFix.gz phastCons scores for 6 species

    phastCons6way.bw  phastCons scores for fish 6 species in bigWig format

    md5sum.txt - md5 check sums of these files to verify correct download files

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/felCat4/multiz6way/

For a description of the phastCons data 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 rsync or ftp rather than downloading the files via our website.
There is approximately 333 MB of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/felCat4/phastCons6way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/felCat4/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.

---------------------------------------------------------------
References for phastCons and phyloP:

Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates
on mammalian phylogenies. Genome Res. 2009 Oct 26. [Epub ahead of print]
(http://genome.cshlp.org/content/early/2009/10/26/gr.097857.109.abstract)

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson
H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements
in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005
Aug;15(8):1034-50.  (http://www.genome.org/cgi/doi/10.1101/gr.3715005)