This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/danRer7/phyloP8way/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 7 vertebrate genomes to the zebrafish genome, plus alternate sets
of scores for a subset of five fish species in the alignments.
Files in this directory are:
vertebrate.mod phyloP tree model with branch lengths
for all 8 species
hg19 mm9 xenTro2 tetNig2 fr2 gasAcu1 oryLat2 danRer7
(human, mouse, X. tropicalis, tetraodon, fugu, stickleback, medaka, zebrafish)
fish.mod phastCons tree model for the fish subset:
tetNig2 fr2 gasAcu1 oryLat2 danRer7
(tetraodon, fugu, stickleback, medaka, zebrafish)
vertebrate.phyloP8way.wigFix.gz phyloP scores for all 8 species
vertebrate.phyloP8way.bw phyloP scores for all 8 species in bigWig format
fish.phyloP8way.wigFix.gz phyloP scores for fish subset
fish.phyloP8way.bw phyloP scores for fish subset in bigWig format
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/danRer7/multiz8way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer7&g=cons8way
Assemblies used in these alignments:
- Human Homo sapiens Feb. 2009 hg19/GRCh37
- Mouse Mus musculus July 2007 mm9
- X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
- Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2
- Fugu Takifugu rubripes Oct. 2004 fr2
- Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
- Medaka Oryzias latipes Oct. 2005 oryLat2
- Zebrafish Danio rerio Jul. 2010 danRer7
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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/danRer7/phyloP8way/ ./
OR
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/danRer7/phyloP8way
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. 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)
Name Last modified Size Description
Parent Directory -
md5sum.txt 2011-10-05 09:45 375
fish.phyloP8way.bw 2011-01-19 12:05 498M
vertebrate.phyloP8way.bw 2011-01-19 12:03 629M
fish.phyloP8way.wigFix.gz 2011-01-19 12:02 264M
vertebrate.phyloP8way.wigFix.gz 2011-01-19 11:59 350M
vertebrate.mod 2011-01-19 11:49 493
fish.mod 2011-01-19 11:48 421