This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/danRer7/phastCons8way/README.txt
This directory contains compressed phastCons scores for multiple alignments
of 7 vertebrate genomes to the zebrafish genome, plus an alternate set
of scores for a subset of five fish species in the alignments.
Files in this directory are:
vertebrate.mod phastCons tree model with branch lengths
for all 8 species
hg19 mm9 xenTro2 tetNig2 fr2 gasAcu1 oryLat2 danRer7
(human, mouse, X. tropicalis, tetraodon, fugu, stickleback, medaka, zebrafish)
fish.mod phastCons tree model for the fish subset:
tetNig2 fr2 gasAcu1 oryLat2 danRer7
(tetraodon, fugu, stickleback, medaka, zebrafish)
vertebrate.phastCons8way.wigFix.gz phastCons scores for 8 species
fish.phastCons8way.wigFix.gz phastCons scores for fish subset
vertebrate.phastCons8way.bw phastCons scores for 8 species in bigWig format
fish.phastCons8way.bw phastCons scores for fish 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/danRer7/multiz8way/
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 Feb. 2009 hg19/GRCh37
- Mouse Mus musculus July 2007 mm9
- 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 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 -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer7/phastCons8way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/danRer7/phastCons8way
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 2011-01-19 12:16 387
fish.phastCons8way.bw 2011-01-19 11:10 756M
fish.phastCons8way.wigFix.gz 2011-01-19 11:03 333M
vertebrate.phastCons8way.bw 2011-01-19 10:53 803M
vertebrate.phastCons8way.wigFix.gz 2011-01-19 10:46 369M
fish.mod 2011-01-19 10:24 451
vertebrate.mod 2011-01-19 10:18 523