This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/petMar2/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 6 vertebrate genomes to the lamprey genome.

Files in this directory:

    petMar2.phyloP7way.mod - phyloP tree model with branch lengths for
                            all 7 species
    petMar2.phyloP7way.bw - scores in bigWig format
    petMar2.phyloP7way.wigFix.gz - scores in fixed step wiggle format

See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
   for bigWig format description

For a description of the fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html

The phastCons data can be found at:
http://hgdownload.cse.ucsc.edu/goldenPath/petMar2/phastCons7way/

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/petMar2/multiz7way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=petMar2&g=cons7way

Assemblies used in these alignments:                                 (alignment
                                                                           type)

Lamprey - Petromyzon marinus        Sep. 2012 (WUGSC 7.0/petMar2)     reference

Chicken - Gallus gallus             Nov. 2011 (ICGSC 4.0/galGal4)       net
Medaka - Oryzias latipes            Oct. 2005 (NIG/UT Medaka1/oryLat2)  net
Opossum - Monodelphis domestica     Oct. 2006 (Broad/monDom5)           net
Human - Homo sapiens                Feb. 2009 (GRCh37/hg19)             net
Mouse - Mus musculus                Dec. 2011 (GRCm38/mm10)             net
Lancelet - Branchiostoma floridae   Apr. 2008 (JGI v2.0/braFlo2)        net

---------------------------------------------------------------
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/petMar2/phyloP7way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/petMar2/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                   2012-11-07 11:42  176   
      petMar2.phyloP7way.bw        2012-11-01 14:51  120M  
      petMar2.phyloP7way.mod       2012-11-01 14:27  475   
      petMar2.phyloP7way.wigFix.gz 2012-11-01 14:49   64M