This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons44way/README.txt
This directory contains compressed phastCons scores for multiple
alignments of 44 vertebrate genomes to the human genome,
plus an alternate set of scores for the primates
subset of species in the alignments, and an alternate set of
scores for the placental mammal subset of species in the alignments.
Files in this directory are:
vertebrate.mod phastCons tree model with branch lengths
for all 44 species
primates.mod phastCons tree model for the primates subset:
hg18, panTro2, gorGor1, ponAbe2, rheMac2, calJac1, tarSyr1, micMur1,
otoGar1
(human, chimp, gorilla, orangutan, rhesus, marmoset, tarsier,
mouse lemur, bushbaby)
placentalMammals.mod phastCons tree model for the placental mammal subset
hg18, panTro2, gorGor1, ponAbe2, rheMac2, calJac1, tarSyr1, micMur1,
otoGar1, tupBel1, mm9, rn4, dipOrd1, cavPor3, speTri1, oryCun1, ochPri2
(human, chimp, gorilla, orangutan, rhesus, marmoset, tarsier,
mouse lemur, bushbaby, tree shrew, mouse, rat, kangaroo rat,
guinea pig, ground squirrel, rabbit, pika)
vertebrate/*.wigFix.gz phastCons scores for 44 species
primates/*.wigFix.gz phastCons scores for primates subset
placentalMammals/*.wigFix.gz phastCons scores for placental mammal subset
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz44way/
For a description of the phastCons data file format, see
http://genome.ucsc.edu/goldenPath/help/phastCons.html
Assemblies used in these alignments:
_ Human Homo sapiens Mar. 2006 hg18
_ 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
_ Marmoset Callithrix jacchus June 2007 calJac1
_ Tarsier Tarsius syrichta Aug. 2008 tarSyr1
_ Mouse lemur Microcebus murinus Jun. 2003 micMur1
_ Bushbaby Otolemur garnettii Dec. 2006 otoGar1
_ TreeShrew Tupaia belangeri Dec. 2006 tupBel1
_ Mouse Mus musculus July 2007 mm9
_ Rat Rattus norvegicus Nov. 2004 rn4
_ Kangaroo rat Dipodomys ordii July 2008 dipOrd1
_ Guinea Pig Cavia porcellus Feb. 2008 cavPor3
_ Squirrel Spermophilus tridecemlineatus Feb. 2008 speTri1
_ Rabbit Oryctolagus cuniculus May 2005 oryCun1
_ Pika Ochotona princeps July 2008 ochPri2
_ Alpaca Vicugna pacos July 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 July 2008 pteVam1
_ Hedgehog Erinaceus europaeus June 2006 eriEur1
_ Shrew Sorex araneus June 2006 sorAra1
_ Elephant Loxodonta africana July 2008 loxAfr2
_ Rock hyrax Procavia capensis July 2008 proCap1
_ Tenrec Echinops telfairi July 2005 echTel1
_ Armadillo Dasypus novemcinctus July 2008 dasNov2
_ Sloth Choloepus hoffmanni July 2008 choHof1
_ Opossum Monodelphis domestica Jan. 2006 monDom4
_ Platypus Ornithorhynchus anatinus Mar. 2007 ornAna1
_ Chicken Gallus gallus May 2006 galGal3
_ Zebra finch Taeniopygia guttata July 2008 taeGut1
_ Lizard Anolis carolinensis Feb. 2007 anoCar1
_ X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2
_ Tetraodon Tetraodon nigroviridis Feb. 2004 tetNig1
_ Fugu Takifugu rubripes Oct. 2004 fr2
_ Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1
_ Medaka Oryzias latipes Oct. 2005 oryLat2
_ Zebrafish Danio rerio July 2007 danRer5
_ Lamprey Petromyzon marinus Mar. 2007 petMar1
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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 -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons44way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/hg18/phastCons44way
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:
Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M.,
Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S.,
Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W.,
and Haussler, D. Evolutionarily conserved elements in vertebrate, insect,
worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
(http://www.genome.org/cgi/doi/10.1101/gr.3715005)
Siepel, A. and Haussler, D. Phylogenetic hidden Markov models.
In R. Nielsen, ed., Statistical Methods in Molecular Evolution,
Springer (in press) (2004).
Name Last modified Size Description
Parent Directory -
vertebrate.mod 2009-01-05 20:46 1.5K
primates.mod 2009-01-13 11:11 534
placentalMammals.mod 2009-01-13 11:21 1.1K
placentalMammals/ 2009-01-27 10:28 -
vertebrate/ 2009-01-27 10:28 -
primates/ 2009-01-27 10:28 -