This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/phastCons9way/README.txt
This directory contains compressed phastCons scores for multiple alignments
of 8 vertebrate genomes to the X. tropicalis genome.
Files in this directory are:
vertebrate.mod phastCons 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)
phastCons9way.wigFix.gz phastCons scores for 9 species, wiggle fixed step
phastCons9way.bw phastCons scores for 9 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/xenTro3/multiz9way/
For a description of the phastCons data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
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.
There is approximately 910 Mb of compressed data in this directory.
Via rsync:
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/phastCons9way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/xenTro3/phastCons9way
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 10:12 203
vertebrate.mod 2011-09-28 16:02 560
phastCons9way.wigFix.gz 2011-09-29 11:37 283M
phastCons9way.bw 2011-09-29 11:40 626M