This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/fr3/phyloP8way/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 7 fish genomes to the Fugu genome.
Files in this directory are:
fish.mod - phyloP tree model with branch lengths for all 8 species:
fugu, tetraodon, nile tilapia, stickleback, medaka,
atlantic cod, zebrafish, coelacanth)
phyloP8way.wigFix.gz phyloP scores for all 8 species, wiggle fixed step
phyloP8way.bw phyloP scores for all 8 species in bigWig format
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/fr3/multiz8way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=fr3&g=cons8way
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
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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 1.8 Gb of compressed data in this directory.
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/phyloP8way/ ./
OR
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/fr3/phyloP8way
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 2012-02-23 13:43 191
fish.mod 2012-02-22 12:03 505
phyloP8way.wigFix.gz 2012-02-22 15:43 457M
phyloP8way.bw 2012-02-22 16:04 782M