This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/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 human genome.
Files in this directory:
hg38.phyloP7way.mod - phyloP tree model with branch lengths for
all 7 species
hg38.phyloP7way.bw - scores in bigWig format
hg38.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/hg38/phastCons7way/
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz7way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons7way
Assemblies used in these alignments: (alignment
type)
Human - Homo sapiens Dec. 2013 (GRCh38/hg38) reference
Chimp - Pan troglodytes Feb. 2011 (GSAC 2.1.4/panTro4) syntenic
Rhesus - Macaca mulatta Oct. 2010 (BGI CR_1.0/rheMac3) syntenic
Dog - Canis lupus familiaris Sep. 2011 (Broad/canFam3) syntenic
Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) syntenic
Rat - Rattus norvegicus Mar. 2012 (RGSC Rnor 5.0/rn5) syntenic
Opossum - Monodelphis domestica Oct. 2006 (Broad/monDom5) 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:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP7way/ ./
OR
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/hg38/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.
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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.
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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)
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Name Last modified Size Description
Parent Directory -
md5sum.txt 2014-06-05 14:25 167
hg38.phyloP7way.bw 2014-06-04 15:04 5.3G
hg38.phyloP7way.wigFix.gz 2014-06-04 14:21 2.9G
hg38.phyloP7way.mod 2014-06-04 13:29 480