This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/danRer7/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 vertebrate genomes to the zebrafish genome, plus alternate sets
of scores for a subset of five fish species in the alignments.

Files in this directory are:
    vertebrate.mod      phyloP tree model with branch lengths
                        for all 8 species
		hg19 mm9 xenTro2 tetNig2 fr2 gasAcu1 oryLat2 danRer7
  (human, mouse, X. tropicalis, tetraodon, fugu, stickleback, medaka, zebrafish)
    fish.mod            phastCons tree model for the fish subset:
		tetNig2 fr2 gasAcu1 oryLat2 danRer7
		(tetraodon, fugu, stickleback, medaka, zebrafish)

    vertebrate.phyloP8way.wigFix.gz phyloP scores for all 8 species
    vertebrate.phyloP8way.bw phyloP scores for all 8 species in bigWig format
    fish.phyloP8way.wigFix.gz  phyloP scores for fish subset
    fish.phyloP8way.bw  phyloP scores for fish subset in bigWig format

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/danRer7/multiz8way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer7&g=cons8way

Assemblies used in these alignments:

  - Human         Homo sapiens                  Feb. 2009  hg19/GRCh37
  - Mouse         Mus musculus                  July 2007  mm9   
  - X. tropicalis Xenopus tropicalis            Aug. 2005  xenTro2
  - Tetraodon     Tetraodon nigroviridis        Mar. 2007  tetNig2
  - Fugu          Takifugu rubripes             Oct. 2004  fr2   
  - Stickleback   Gasterosteus aculeatus        Feb. 2006  gasAcu1
  - Medaka        Oryzias latipes               Oct. 2005  oryLat2
  - Zebrafish     Danio rerio                   Jul. 2010  danRer7

---------------------------------------------------------------
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 -avz --progress \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer7/phyloP8way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/danRer7/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.

---------------------------------------------------------------
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.txt05-Oct-2011 09:42 3.6K 
[SND]fish.mod19-Jan-2011 11:48 421  
[   ]fish.phyloP8way.bw19-Jan-2011 12:05 498M 
[   ]fish.phyloP8way.wigFix.gz19-Jan-2011 12:02 264M 
[TXT]md5sum.txt05-Oct-2011 09:45 375  
[SND]vertebrate.mod19-Jan-2011 11:49 493  
[   ]vertebrate.phyloP8way.bw19-Jan-2011 12:03 629M 
[   ]vertebrate.phyloP8way.wigFix.gz19-Jan-2011 11:59 350M 

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