This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/felCat4/phyloP6way/README.txt

This directory contains conservation scoring by phyloP (phylogenetic p-values)
from the PHAST package (http://compgen.bscb.cornell.edu/phast/) 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      phyloP tree model with branch lengths
                 for all 6 species
                 (felCat4, canFam2, ailMel1, hg19, mm9 monDom5)
 
    phyloP6way.wigFix.gz  phyloP scores for all 6 species
   
    phyloP6way.bw   phyloP scores for all 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 more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=felCat4&g=cons6way


---------------------------------------------------------------
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:

   rsync -avz --progress \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/felCat4/phyloP6way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/felCat4/phyloP6way

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 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)

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      phyloP6way.bw           2011-01-21 22:51  3.4G  
      phyloP6way.wigFix.gz    2011-01-21 14:53  1.9G  
      all.mod                 2011-01-21 09:29  451   
      md5sum.txt              2011-01-27 09:32  190