This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/rn5/phyloP13way/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 13 vertebrate genomes to the rat genome.

Files in this directory are:

    rn5.phyloP.13way.mod - phyloP tree model with branch lengths for all 13 species

PhyloP scores in bigWig format files:
    rn5.13way.phyloP13way.bw
See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
   for bigWig format description

PhyloP scores in fixed step wiggle format:
    phyloP13way.wigFix.gz - phyloP scores for all 13 species

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/rn5/phastCons13way/

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/rn5/multiz13way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rn5&g=cons13way

Assemblies used in these alignments:

Rat                      Rattus norvegicus              Mar 2012  RGSC 5.0/rn5                                  Reference species
Chicken                  Gallus gallus                  Nov 2011  ICGSC Gallus_gallus-4.0/galGal4               Net
Chimp                    Pan troglodytes                Feb 2011  CSAC 2.1.4/panTro4                            Syntenic net
Cow                      Bos taurus                     Oct 2011  Baylor Btau_4.6.1/bosTau7                     Syntenic net
Dog                      Canis lupus familiaris         Sep 2011  Broad CanFam3.1/canFam3                       Syntenic net
Guinea pig               Cavia porcellus                Feb 2008  Broad/cavPor3                                 Syntenic net
Human                    Homo sapiens                   Dec 2013  GRCh38/hg38                                   Syntenic net
Mouse                    Mus musculus                   Dec 2011  GRCm38/mm10                                   Syntenic net
Opossum                  Monodelphis domestica          Oct 2006  Broad/monDom5                                 Net
Panda                    Ailuropoda melanoleuca         Dec 2009  BGI-Shenzhen 1.0/ailMel1                      Reciprocal best
Rhesus                   Macaca mulatta                 Oct 2010  BGI CR_1.0/rheMac3                            Syntenic net
Turkey                   Meleagris gallopavo            Dec 2009  TGC Turkey_2.01/melGal1                       Net
Zebrafish                Danio rerio                    Jul 2010  Zv9/danRer7                                   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.
There is approximately 6.7 Gb of compressed data in this directory.:

Via rsync:
rsync -avz --progress \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/rn5/phyloP13way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/rn5/phyloP13way

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. 2010 Jan;20(1):110-21.
(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://genome.cshlp.org/content/15/8/1034)