This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/panTro3/phyloP12way/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 11 vertebrate genomes to the chimp genome, plus alternate sets
of scores for a subset of five primate species in the alignments.

Files in this directory are:
    vertebrate.mod      phyloP tree model with branch lengths
                        for all 12 species
		panTro3 hg19 ponAbe2 rheMac2 calJac3 equCab2 canfam2 mm9 rn4
		monDom5 galGal3 danRer7
		  (chimp, human, orangutan, rhesus, marmoset, horse, dog,
			mouse, rat, opossum chicken, zebrafish)
    primate.mod            phyloP tree model for the primate subset:
		panTro3 hg19 ponAbe2 rheMac2 calJac3
		(chimp, human, orangutan, rhesus, marmoset)

    vertebrate.phyloP12way.wigFix.gz phyloP scores for all 12 species
    primate.phyloP12way.wigFix.gz  phyloP scores for primate subset
    vertebrate.phyloP12way.bw phyloP scores for all 12 species in bigWig format
    primate.phyloP12way.bw  phyloP scores for primate subset in bigWig format

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/panTro3/multiz12way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=panTro3&g=cons12way

Assemblies used in these alignments:

  - Chimp         Pan troglodytes               Oct. 2010  panTro3
  - Human         Homo sapiens                  Feb. 2009  hg19/GRCh37
  - Orangutan     Pongo pygmaeus abelii         July 2007  ponAbe2   
  - Rhesus        Macaca mulatta                Jan. 2006  rheMac2   
  - Marmoset      Callithrix jacchus            Mar. 2009  calJac3   
  - Horse         Equus caballus                Sep. 2007  equCab2   
  - Dog           Canis lupus familiaris        May. 2005  canFam2   
  - Mouse         Mus musculus                  July 2007  mm9   
  - Rat           Rattus norvegicus             Nov. 2004  rn4
  - Opossum       Monodelphis domestica         Oct. 2006  monDom5
  - Chicken       Gallus gallus                 May. 2006  galGal3
  - Zebrafish     Danio rerio                   Jul. 2010  danRer7

---------------------------------------------------------------
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/panTro3/phyloP12way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/panTro3/phyloP12way

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)