This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/phyloP7way/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 7 vertebrate genomes to the lizard genome.

Files in this directory are:
    vertebrate.mod      phyloP tree model with branch lengths
                        for all 7 species
		anoCar2 galGal3 ornAna1 hg19 mm9 xenTro2 gasAcu1
	  (lizard, chicken, platypus, human, mouse, X. tropicalis, stickleback)

    phyloP7way.wigFix.gz phyloP scores for all 7 species, wiggle fixed step
    phyloP7way.bw phyloP scores for all 7 species in bigWig format

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/multiz7way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=anoCar2&g=cons7way

Assemblies used in these alignments:

  - Lizard         Anolis carolinensis        May  2010  anoCar2/Broad
  - Chicken        Gallus gallus              May  2006  galGal3/WUGSC 2.1
  - Platypus       Ornithorhynchus anatinus   Mar. 2007  ornAna1/WUGSC 5.0.1
  - Human          Homo sapiens               Feb. 2009  hg19/GRCh37   
  - Mouse          Mus musculus               July 2007  mm9/NCBI37
  - X. tropicalis  Xenopus tropicalis         Aug. 2005  xenTro2/JGI 4.1
  - Stickleback    Gasterosteus aculeatus     Feb. 2006  gasAcu1/Broad

---------------------------------------------------------------
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 -av --progress \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/phyloP7way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/anoCar2/phyloP7way

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                             -   
      md5sum.txt              2011-05-17 15:34  197   
      phyloP7way.bw           2011-05-17 13:24  485M  
      phyloP7way.wigFix.gz    2011-05-17 13:18  260M  
      vertebrate.mod          2011-05-17 12:38  474