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)
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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.
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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)
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Name Last modified Size Description
Parent Directory -
md5sum.txt 2017-01-24 14:45 167
rn6.phyloP20way.bw 2017-01-23 20:16 5.3G
rn6.phyloP20way.mod 2017-01-23 11:14 854
rn6.phyloP20way.wigFix.gz 2017-01-23 13:44 3.1G