This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/danRer6/phastCons6way/README.txt

This directory contains compressed phastCons scores for multiple alignments
of 6 vertebrate genomes to the zebrafish genome.

Files in this directory are:
    all.mod      phastCons tree model with branch lengths
                        for all 6 species

    phastCons6way.wigFix.gz phastCons scores for 6 species

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/danRer6/multiz6way/

For a description of the phastCons data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html

Assemblies used in these alignments:

  - Zebrafish     Danio rerio                   Dec. 2008  danRer6
  - Tetraodon     Tetraodon nigroviridis        Mar. 2007  tetNig2
  - Stickleback   Gasterosteus aculeatus        Feb. 2006  gasAcu1
  - X. tropicalis Xenopus tropicalis            Aug. 2005  xenTro2
  - Mouse         Mus musculus                  July 2007  mm9
  - Human         Homo sapiens                  Feb. 2009  hg19/GRCh37


---------------------------------------------------------------
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 333 MB of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer6/phastCons6way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/danRer6/phastCons6way

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.txt29-Jun-2010 13:55 2.8K 
[SND]all.mod21-May-2010 00:13 476  
[TXT]md5sum.txt13-Jul-2010 16:41 100  
[   ]phastCons6way.wigFix.gz24-May-2010 17:31 333M 

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