This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/phyloP9way/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 9 vertebrate genomes to the X. tropicalis genome.
Files in this directory are:
vertebrate.mod phyloP tree model with branch lengths
for all 9 species
xenTro3 anoCar2 galGal3 melGal1 monDom5 rn4 mm9 hg19 danRer7
(X. tropicalis, lizard, chicken, turkey, opossum, rat, mouse, human,
zebrafish)
phyloP9way.wigFix.gz phyloP scores for all 9 species, wiggle fixed step
phyloP9way.bw phyloP scores for all 9 species in bigWig format
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/multiz9way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro3&g=cons9way
Assemblies used in these alignments:
- X. tropicalis Xenopus tropicalis Nov. 2009 xenTro3/JGI 4.2
- Lizard Anolis carolinensis May 2010 anoCar2/Broad
- Chicken Gallus gallus May 2006 galGal3/WUGSC 2.1
- Turkey Meleagris gallopavo Dec. 2009 melGal1/TGC Turkey_2.01
- Opossum Monodelphis domestica Oct. 2006 monDom5/Broad
- Rat Rattus norvegicus Nov. 2004 rn4/Baylor 3.4
- Mouse Mus musculus Jul. 2007 mm9/NCBI37
- Human Homo sapiens Feb. 2009 hg19/GRCh37
- Zebrafish Danio rerio Jul. 2010 danRer7/Zv9
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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:
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/phyloP9way/ ./
OR
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/xenTro3/phyloP9way
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 2011-09-30 10:15 197
phyloP9way.bw 2011-09-29 15:01 498M
phyloP9way.wigFix.gz 2011-09-29 14:56 274M
vertebrate.mod 2011-09-29 13:08 529