This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/fr3/phastCons8way/README.txt
This directory contains compressed phastCons scores for multiple alignments
of 7 fish genomes to the Fugu genome.
Files in this directory are:
fish.mod - phastCons tree model with branch lengths for all 8 species:
fugu, tetraodon, nile tilapia, stickleback, medaka,
atlantic cod, zebrafish, coelacanth)
phastCons8way.wigFix.gz phastCons scores for 8 species, wiggle fixed step
phastCons8way.bw phastCons scores for 8 species 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/fr3/multiz8way/
For a description of the phastCons data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
Assemblies used in these alignments:
Fugu Takifugu rubripes Oct. 2011 FUGU5/fr3
Tetraodon Tetraodon nigroviridis Mar. 2007 Genoscope 8.0/tetNig2
Nile tilapia Oreochromis niloticus Jan. 2011 Broad/oreNil1
Stickleback Gasterosteus aculeatus Feb. 2006 Broad/gasAcu1
Atlantic cod Gadus morhua May. 2010 Genofisk/gadMor1
Medaka Oryzias latipes Oct. 2005 NIG/oryLat2
Zebrafish Danio rerio Jul. 2010 Zv9/danRer7
Coelacanth Latimeria chalumnae Aug. 2011 Broad/latCha1
---------------------------------------------------------------
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 1.7 Gb of compressed data in this directory.
Via rsync:
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/phastCons8way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/fr3/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.
---------------------------------------------------------------
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 2012-02-23 13:42 197
phastCons8way.bw 2012-02-22 15:39 778M
phastCons8way.wigFix.gz 2012-02-22 14:01 378M
fish.mod 2012-02-22 10:26 536