This file is from:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/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 45 vertebrate genomes to the human genome, plus alternate sets
of scores for the primate species and the placental mammal species in the
alignments.
Files in this directory are:
vertebrate.mod phyloP tree model with branch lengths
for all 46 species
primates.mod phyloP tree model for the primates subset:
hg19, panTro2, gorGor1, ponAbe2, rheMac2, papHam1, calJac1, tarSyr1,
micMur1, otoGar1
(human, chimp, gorilla, orangutan, rhesus, baboon, marmoset, tarsier,
mouse lemur, bushbaby)
placentalMammals.mod phyloP tree model for the placental mammal subset
hg19, panTro2, gorGor1, ponAbe2, rheMac2, papHam1, calJac1, tarSyr1,
micMur1, otoGar1, tupBel1, mm9, rn4, dipOrd1, cavPor3, speTri1,
oryCun2, ochPri2, vicPac1, turTru1, bosTau4, equCab2, felCat3, canFam2,
myoLuc1, pteVam1, eriEur1, sorAra1, loxAfr3, proCap1, echTel1, dasNov2,
choHof1
(human, chimp, gorilla, orangutan, rhesus, baboon, marmoset, tarsier,
mouse lemur, bushbaby, tree shrew, mouse, rat, kangaroo rat,
guinea pig, ground squirrel, rabbit, pika, alpaca, dolphin, cow,
horse, cat, dog, microbat, megabat, hedgehog, shrew, elephant,
rock hyrax, tenrec, armadillo, sloth)
The models above are calculated only from the chromosomes:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Y
vertebrate.chrX.mod phyloP tree model only for chromosome X
primates.chrX.mod phyloP tree model only for chromosome X
placentalMammals.chrX.mod phyloP tree model only for chromosome X
vertebrate/*.wigFix.gz phyloP scores for all 46 species
primates/*.wigFix.gz phyloP scores for primate subset
placentalMammals/*.wigFix.gz phyloP scores for placental mammal subset
vertebrate.phyloP46way.bw - scores for all 46 species in bigWig format
placentalMammals.phyloP46way.bw - scores for placental mammal subset in bigWig format
primates.phyloP46way.bw - scores for primate subset in bigWig format
md5sum.txt - MD5 checksums to verify download files
See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
for bigWig format description
For a description of the fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
The phastCons data can be found at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/
The multiple alignments and methods description are at:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way
Assemblies used in these alignments:
- Human Homo sapiens Feb. 2009 hg19/GRCh37
- Chimp Pan troglodytes Mar. 2006 panTro2
- Gorilla Gorilla gorilla gorilla Oct. 2008 gorGor1
- Orangutan Pongo pygmaeus abelii July 2007 ponAbe2
- Rhesus Macaca mulatta Jan. 2006 rheMac2
- Baboon Papio hamadryas Nov. 2008 papHam1
- Marmoset Callithrix jacchus June 2007 calJac1
- Tarsier Tarsius syrichta Aug. 2008 tarSyr1
- Mouse lemur Microcebus murinus Jul. 2007 micMur1
- Bushbaby Otolemur garnettii Dec. 2006 otoGar1
- Tree shrew Tupaia belangeri Dec. 2006 tupBel1
- Mouse Mus musculus July 2007 mm9
- Rat Rattus norvegicus Nov. 2004 rn4
- Kangaroo rat Dipodomys ordii Jul. 2008 dipOrd1
- Guinea Pig Cavia porcellus Feb. 2008 cavPor3
- Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1
- Rabbit Oryctolagus cuniculus Apr. 2009 oryCun2
- Pika Ochotona princeps Jul. 2008 ochPri2
- Alpaca Vicugna pacos Jul. 2008 vicPac1
- Dolphin Tursiops truncatus Feb. 2008 turTru1
- Cow Bos taurus Oct. 2007 bosTau4
- Horse Equus caballus Sep. 2007 equCab2
- Cat Felis catus Mar. 2006 felCat3
- Dog Canis lupus familiaris May 2005 canFam2
- Microbat Myotis lucifugus Mar. 2006 myoLuc1
- Megabat Pteropus vampyrus Jul. 2008 pteVam1
- Hedgehog Erinaceus europaeus June 2006 eriEur1
- Shrew Sorex araneus June 2006 sorAra1
- Elephant Loxodonta africana Jul. 2009 loxAfr3
- Rock hyrax Procavia capensis Jul. 2008 proCap1
- Tenrec Echinops telfairi July 2005 echTel1
- Armadillo Dasypus novemcinctus Jul. 2008 dasNov2
- Sloth Choloepus hoffmanni Jul. 2008 choHof1
- Wallaby Macropus eugenii Nov. 2007 macEug1
- Opossum Monodelphis domestica Oct. 2006 monDom5
- Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
- Chicken Gallus gallus May 2006 galGal3
- Zebra finch Taeniopygia guttata Jul. 2008 taeGut1
- Lizard Anolis carolinensis Feb. 2007 anoCar1
- 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 Dec. 2008 danRer6
- Lamprey Petromyzon marinus Mar. 2007 petMar1
---------------------------------------------------------------
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.soe.ucsc.edu/goldenPath/hg19/phyloP46way/ ./
OR
ftp hgdownload.soe.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/hg19/phyloP46way
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 -
md5sum.txt 2021-01-15 09:20 501
placentalMammals.chrX.mod 2009-11-10 13:00 1.2K
placentalMammals.mod 2009-11-10 13:00 1.2K
placentalMammals.phyloP46way.bw 2011-03-29 14:56 8.0G
placentalMammals/ 2009-10-30 11:42 -
primates.chrX.mod 2009-11-10 13:00 564
primates.mod 2009-11-10 13:00 564
primates.phyloP46way.bw 2009-11-10 19:21 20G
primates/ 2009-10-30 11:42 -
vertebrate.chrX.mod 2009-11-10 13:00 1.5K
vertebrate.mod 2009-11-10 13:00 1.5K
vertebrate.phyloP46way.bw 2009-11-10 19:27 20G
vertebrate/ 2009-10-30 11:41 -