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

---------------------------------------------------------------
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.

---------------------------------------------------------------
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)

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt04-Jan-2012 09:22 2.9K 
[TXT]md5sum.txt04-Jan-2012 09:22 1.1K 
[SND]sacCer3.7way.tree.mod01-Sep-2011 17:08 472  
[   ]sacCer3.chrI.wigFixed.gz02-Sep-2011 10:03 276K 
[   ]sacCer3.chrII.wigFixed.gz02-Sep-2011 10:03 1.0M 
[   ]sacCer3.chrIII.wigFixed.gz02-Sep-2011 10:03 388K 
[   ]sacCer3.chrIV.wigFixed.gz02-Sep-2011 10:03 1.8M 
[   ]sacCer3.chrIX.wigFixed.gz02-Sep-2011 10:03 542K 
[   ]sacCer3.chrM.wigFixed.gz02-Sep-2011 10:03 90K 
[   ]sacCer3.chrV.wigFixed.gz02-Sep-2011 10:03 679K 
[   ]sacCer3.chrVI.wigFixed.gz02-Sep-2011 10:03 323K 
[   ]sacCer3.chrVII.wigFixed.gz02-Sep-2011 10:03 1.3M 
[   ]sacCer3.chrVIII.wigFixed.gz02-Sep-2011 10:03 678K 
[   ]sacCer3.chrX.wigFixed.gz02-Sep-2011 10:06 921K 
[   ]sacCer3.chrXI.wigFixed.gz02-Sep-2011 10:06 822K 
[   ]sacCer3.chrXII.wigFixed.gz02-Sep-2011 10:06 1.3M 
[   ]sacCer3.chrXIII.wigFixed.gz02-Sep-2011 10:06 1.1M 
[   ]sacCer3.chrXIV.wigFixed.gz02-Sep-2011 10:06 968K 
[   ]sacCer3.chrXV.wigFixed.gz02-Sep-2011 10:06 1.3M 
[   ]sacCer3.chrXVI.wigFixed.gz02-Sep-2011 10:06 1.1M 
[   ]sacCer3.phastCons7way.bw02-Sep-2011 10:16 29M 

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