This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/phastCons7way/README.txt
This directory contains compressed phastCons scores for multiple alignments
of 6 yeast genomes to the the S. cerevisiae genome (sacCer3, April 2011):
Files in this directory:
sacCer3.7way.tree.mod - phastCons tree model with branch lengths
for all 7 species
sacCer3.chr*.wigFixed.gz - phastCons scores for the 7 species,
wiggle fixed step format
sacCer3.phastCons7way.bw phastCons scores for the 7 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/sacCer3/multiz7way/
For a description of the phastCons data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
http://genome.ucsc.edu/goldenPath/help/wiggle.html
Assemblies used in these alignments:
- S. cerevisiae S. cerevisiae
- S. paradoxus S. paradoxus
- S. mikatae S. mikatae
- S. kudriavzevii S. kudriavzevii
- S. bayanus S. bayanus
- S. castelli S. castelli
- S. kluyveri S. kluyveri
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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 100 Mb of data in this directory when uncompressed.
Via rsync:
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/phastCons7way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/sacCer3/phastCons7way
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 2012-01-04 09:22 1.1K
sacCer3.7way.tree.mod 2011-09-01 17:08 472
sacCer3.chrI.wigFixed.gz 2011-09-02 10:03 276K
sacCer3.chrII.wigFixed.gz 2011-09-02 10:03 1.0M
sacCer3.chrIII.wigFixed.gz 2011-09-02 10:03 388K
sacCer3.chrIV.wigFixed.gz 2011-09-02 10:03 1.8M
sacCer3.chrIX.wigFixed.gz 2011-09-02 10:03 542K
sacCer3.chrM.wigFixed.gz 2011-09-02 10:03 90K
sacCer3.chrV.wigFixed.gz 2011-09-02 10:03 679K
sacCer3.chrVI.wigFixed.gz 2011-09-02 10:03 323K
sacCer3.chrVII.wigFixed.gz 2011-09-02 10:03 1.3M
sacCer3.chrVIII.wigFixed.gz 2011-09-02 10:03 678K
sacCer3.chrX.wigFixed.gz 2011-09-02 10:06 921K
sacCer3.chrXI.wigFixed.gz 2011-09-02 10:06 822K
sacCer3.chrXII.wigFixed.gz 2011-09-02 10:06 1.3M
sacCer3.chrXIII.wigFixed.gz 2011-09-02 10:06 1.1M
sacCer3.chrXIV.wigFixed.gz 2011-09-02 10:06 968K
sacCer3.chrXV.wigFixed.gz 2011-09-02 10:06 1.3M
sacCer3.chrXVI.wigFixed.gz 2011-09-02 10:06 1.1M
sacCer3.phastCons7way.bw 2011-09-02 10:16 29M