This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/panTro3/phastCons12way/README.txt
This directory contains compressed phastCons scores for multiple alignments
of 11 vertebrate genomes to the chimp genome, plus an alternate set
of scores for a subset of five primate species in the alignments.
Files in this directory are:
vertebrate.mod phastCons 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 phastCons tree model for the primate subset:
panTro3 hg19 ponAbe2 rheMac2 calJac3
(chimp, human, orangutan, rhesus, marmoset)
vertebrate.phastCons12way.wigFix.gz phastCons scores for 12 species
primate.phastCons12way.wigFix.gz phastCons scores for primate subset
vertebrate.phastCons12way.bw phastCons scores for 12 species in bigWig format
primate.phastCons12way.bw phastCons scores for primate subset in bigWig format
md5sum.txt - md5 check sums of these files to verify correct download files
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/panTro3/multiz12way/
For a description of the phastCons data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
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.
There is approximately 8.5 Gb of compressed data in this directory.
Via rsync:
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro3/phastCons12way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/panTro3/phastCons12way
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 2011-05-06 14:47 400
primate.phastCons12way.bw 2011-03-29 14:44 7.5G
vertebrate.phastCons12way.bw 2011-03-29 14:44 6.4G
primate.phastCons12way.wigFix.gz 2011-03-28 13:18 3.7G
vertebrate.phastCons12way.wigFix.gz 2011-03-28 12:12 3.1G
primate.mod 2011-03-28 10:27 459
vertebrate.mod 2011-03-28 10:13 653