This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/rn6/phyloP20way/README.txt

This directory contains conversation scoring by phyloP (phylogenetic p-values)
from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple
alignments of 19 genomes to the rat genome.

Files in this directory are:

    rn6.phyloP20way.mod  phyloP tree model with branch lengths
                        for the 20 genomes
    rn6.phyloP20way.wigFix.gz - phyloP scores for the 20 genomes
                                 in fixed step wiggle format
    rn6.phyloP20way.bw - phyloP scores for the 20 species
                          in bigWig format
    md5sum.txt - md5 sums of the files here to verify accurate download

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/rn6/multiz20way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rn6&g=cons20way

For a description of the phyloP wigFix data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
see also the section describing the 'fixedStep' wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html

Assemblies used in these alignments:

rat - Rattus norvegicus - Jul. 2014 (RGSC 6.0/rn6) reference

Rat             Rattus norvegicus        Jul. 2014 (RGSC 6.0/rn6)

Mouse           Mus musculus             Dec. 2011 (GRCm38/mm10)
Prairie vole    Microtus ochrogaster     Oct. 2012 (MicOch1.0/micOch1)
Guinea pig      Cavia porcellus          Feb. 2008 (Broad/cavPor3)
Rabbit          Oryctolagus cuniculus    Apr. 2009 (Broad/oryCun2)
Human           Homo sapiens             Dec. 2013 (GRCh38/hg38)
Chimp           Pan troglodytes          May  2016 (Pan_tro 3.0/panTro5)
Rhesus          Macaca mulatta           Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
Tarsier         Tarsius syrichta         Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)
Dog             Canis lupus familiaris   Sep. 2011 (Broad CanFam3.1/canFam3)
Panda           Ailuropoda melanoleuca   Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)
Cat             Felis catus              Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)
Cow             Bos taurus               Jun. 2014 (Bos_taurus_UMD_3.1.1/bosTau8)
Opossum         Monodelphis domestica    Oct. 2006 (Broad/monDom5)
Platypus        Ornithorhynchus anatinus Feb. 2007 (ASM227v2/ornAna2)
Chicken         Gallus gallus            Dec. 2015 (Gallus_gallus-5.0/galGal5)
Turkey          Meleagris gallopavo      Nov. 2014 (Turkey_5.0/melGal5)
X. tropicalis   Xenopus tropicalis       Sep. 2012 (JGI 7.0/xenTro7)
Zebrafish       Danio rerio              Sep. 2014 (GRCz10/danRer10)
Elephant shark  Callorhinchus milii      Dec. 2013 (Callorhinchus_milii-6.1.3/calMil1)

---------------------------------------------------------------
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 8.5 Gb of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/rn6/phyloP20way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/rn6/phyloP20way

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, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates
on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21.
(http://genome.cshlp.org/content/20/1/110.long)

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.full)

---------------------------------------------------------------
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt30-Jan-2017 11:54 4.5K 
[TXT]md5sum.txt24-Jan-2017 14:45 167  
[   ]rn6.phyloP20way.bw23-Jan-2017 20:16 5.3G 
[SND]rn6.phyloP20way.mod23-Jan-2017 11:14 854  
[   ]rn6.phyloP20way.wigFix.gz23-Jan-2017 13:44 3.1G 

Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80