This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/panTro3/phyloP12way/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 11 vertebrate genomes to the chimp genome, plus alternate sets
of scores for a subset of five primate species in the alignments.
Files in this directory are:
vertebrate.mod phyloP tree model with branch lengths
for all 12 species
panTro3 hg19 ponAbe2 rheMac2 calJac3 equCab2 canfam2 mm9 rn4
monDom5 galGal3 danRer7
(chimp, human, orangutan, rhesus, marmoset, horse, dog,
mouse, rat, opossum chicken, zebrafish)
primate.mod phyloP tree model for the primate subset:
panTro3 hg19 ponAbe2 rheMac2 calJac3
(chimp, human, orangutan, rhesus, marmoset)
vertebrate.phyloP12way.wigFix.gz phyloP scores for all 12 species
primate.phyloP12way.wigFix.gz phyloP scores for primate subset
vertebrate.phyloP12way.bw phyloP scores for all 12 species in bigWig format
primate.phyloP12way.bw phyloP scores for primate subset in bigWig format
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/panTro3/multiz12way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=panTro3&g=cons12way
Assemblies used in these alignments:
- Chimp Pan troglodytes Oct. 2010 panTro3
- Human Homo sapiens Feb. 2009 hg19/GRCh37
- Orangutan Pongo pygmaeus abelii July 2007 ponAbe2
- Rhesus Macaca mulatta Jan. 2006 rheMac2
- Marmoset Callithrix jacchus Mar. 2009 calJac3
- Horse Equus caballus Sep. 2007 equCab2
- Dog Canis lupus familiaris May. 2005 canFam2
- Mouse Mus musculus July 2007 mm9
- Rat Rattus norvegicus Nov. 2004 rn4
- Opossum Monodelphis domestica Oct. 2006 monDom5
- Chicken Gallus gallus May. 2006 galGal3
- 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 -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro3/phyloP12way/ ./
OR
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/panTro3/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.
---------------------------------------------------------------
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 -
vertebrate.phyloP12way.bw 2011-03-30 10:21 5.9G
primate.phyloP12way.bw 2011-03-30 10:19 4.0G
vertebrate.phyloP12way.wigFix.gz 2011-03-29 16:07 3.4G
primate.phyloP12way.wigFix.gz 2011-03-29 16:00 2.0G
vertebrate.mod 2011-03-29 10:00 622
primate.mod 2011-03-29 10:00 429
md5sum.txt 2011-05-06 14:46 388