This file is from:
http://hgdownload.soe.ucsc.edu/goldenPath/danRer10/phyloP12way/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 11 genomes to the
Danio rerio/danRer10/Sept. 2014 zebrafish genome.
Files in this directory are:
danRer10.phyloP12way.mod phyloP tree model with branch lengths
for all the sequences
danRer10.12way.phyloP/*.wigFix.gz - phyloP scores for all the alignments
in fixed step wiggle format
danRer10.phyloP12way.bw - phyloP scores for all the alignments
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.soe.ucsc.edu/goldenPath/danRer10/multiz12way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer10&g=cons12way
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:
Zebrafish Danio rerio Sep. 2014 (GRCz10/danRer10) (reference)
Stickleback Gasterosteus aculeatus Feb. 2006 (Broad/gasAcu1) (maf net)
Medaka Oryzias latipes Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (maf net)
Tetraodon Tetraodon nigroviridis Mar. 2007
(Genoscope 8.0/tetNig2) (maf net)
Fugu Takifugu rubripes Oct. 2011 (FUGU5/fr3) (maf net)
Spotted gar Lepisosteus oculatus Dec 2011 (LepOcu1/lepOcu1) (maf net)
Human Homo sapiens Dec. 2013 (GRCh38/hg38) (maf net)
Mouse Mus musculus Dec. 2011 (GRCm38/mm10) (maf net)
Chicken Gallus gallus Mar. 2018 (GRCg6a/galGal6) (maf net)
X. tropicalis Xenopus tropicalis Jul. 2016
(Xenopus_tropicalis_v9.1/xenTro9) (maf net)
Coelacanth Latimeria chalumnae Aug. 2011 (Broad/latCha1) (maf net)
Elephant shark Callorhinchus milii Dec. 2013
(Callorhinchus_milii-6.1.3/calMil1) (maf 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 5.8 Gb of compressed data in this directory,
approximately 10 Gb uncompressed..
Via rsync:
rsync -avz --progress \
rsync://hgdownload.soe.ucsc.edu/goldenPath/galGal6/phyloP12way/ ./
Via FTP:
ftp hgdownload.soe.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/galGal6/phyloP12way
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/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 -
danRer10.phyloP12way.bw 2020-03-18 14:29 774M
danRer10.phyloP12way.mod 2020-03-18 12:29 615
danRer10.phyloP12way.wigFix.gz 2020-03-18 14:21 441M
md5sum.txt 2020-03-18 15:45 182