This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/phyloP11way/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 10 primate genomes to the Gorilla genome.
Files in this directory are:
primate.mod phyloP tree model with branch lengths for all 11 species
gorilla, chimp, human, gibbon, orangutan, baboon,
rhesus, marmoset, tarsier, mouse lemur, bushbaby
(gorGor3, panTro3, hg19, nomLeu1, ponAbe2, papHam1,
rheMac2, calJac3, tarSyr1, micMur1, otoGar1)
phyloP11way.wigFix.gz phyloP scores for all 11 species, wiggle fixed step
phyloP11way.bw phyloP scores for all 11 species in bigWig format
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/multiz11way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=gorGor3&g=cons11way
Assemblies used in these alignments:
Gorilla gorilla gorilla May 2011 Sanger gorGor3.1/gorGor3
Chimp Pan troglodytes Oct. 2010 CGSC 2.1.3/panTro3
Human Homo sapiens Feb. 2009 GRCh37/hg19
Gibbon Nomascus leucogenys Jan. 2010 GGSC Nleu1.0/nomLeu1
Orangutan Pongo pygmaeus abelii Jul. 2007 WUGSC 2.0.2/ponAbe2
Baboon Papio hamadryas Nov. 2008 Baylor 1.0/papHam1
Rhesus Macaca mulatta Jan. 2006 MGSC Merged 1.0/rheMac2
Marmoset Callithrix jacchus Mar. 2009 WUGSC 3.2/calJac3
Tarsier Tarsius syrichta Aug. 2008 Broad/tarSyr1
Mouse lemur Microcebus murinus Jun. 2003 Broad/micMur1
Bushbaby Otolemur garnettii Dec. 2006 Broad/otoGar1
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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/gorGor3/phyloP11way/ ./
OR
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/gorGor3/phyloP11way
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)
Name Last modified Size Description
Parent Directory -
md5sum.txt 2011-12-08 11:09 196
primate.mod 2011-12-07 09:53 616
phyloP11way.wigFix.gz 2011-12-07 12:00 2.4G
phyloP11way.bw 2011-12-07 14:30 4.5G