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
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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 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.
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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, 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)
Name Last modified Size Description
Parent Directory -
md5sum.txt 2014-06-19 16:46 220
phyloP13way.wigFix.gz 2014-04-30 15:18 2.4G
rn5.13way.phyloP13way.bw 2014-04-30 16:11 4.2G
rn5.13way.phyloP13way.mod 2014-04-24 16:58 652