This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/phyloP9way/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 9 vertebrate genomes to the X. tropicalis genome.

Files in this directory are:
    vertebrate.mod      phyloP tree model with branch lengths
                        for all 9 species
          xenTro3 anoCar2 galGal3 melGal1 monDom5 rn4 mm9 hg19 danRer7
    (X. tropicalis, lizard, chicken, turkey, opossum, rat, mouse, human,
	zebrafish)

    phyloP9way.wigFix.gz phyloP scores for all 9 species, wiggle fixed step
    phyloP9way.bw phyloP scores for all 9 species in bigWig format

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/multiz9way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro3&g=cons9way

Assemblies used in these alignments:

 - X. tropicalis  Xenopus tropicalis         Nov. 2009  xenTro3/JGI 4.2
 - Lizard         Anolis carolinensis        May  2010  anoCar2/Broad
 - Chicken        Gallus gallus              May  2006  galGal3/WUGSC 2.1
 - Turkey         Meleagris gallopavo        Dec. 2009  melGal1/TGC Turkey_2.01
 - Opossum        Monodelphis domestica      Oct. 2006  monDom5/Broad
 - Rat            Rattus norvegicus          Nov. 2004  rn4/Baylor 3.4
 - Mouse          Mus musculus               Jul. 2007  mm9/NCBI37
 - Human          Homo sapiens               Feb. 2009  hg19/GRCh37   
 - Zebrafish      Danio rerio                Jul. 2010  danRer7/Zv9

---------------------------------------------------------------
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/xenTro3/phyloP9way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/xenTro3/phyloP9way

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)