This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/phastCons11way/README.txt

This directory contains compressed phastCons scores for multiple alignments
of 10 vertebrate genomes to the Gorilla genome.

Files in this directory are:
    primate.mod - phastCons tree model with branch lengths for all 11 species:
                        gorilla, chimp, human, gibbon, orangutan, baboon,
                        rhesus, marmoset, tarsier, mouse lemur, bushbaby
			(gorGor3, panTro3, hg19, nomLeu1, ponAbe2, papHam1,
			rheMac2, calJac3, tarSyr1, micMur1, otoGar1)

    phastCons11way.wigFix.gz phastCons scores for 11 species, wiggle fixed step
    phastCons11way.bw phastCons scores for 11 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/gorGor3/multiz11way/

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

Assemblies used in these alignments:

Gorilla gorilla gorilla                 May  2011   Sanger gorGor3.1/gorGor3
Chimp           Pan troglodytes         Oct. 2010   CGSC 2.1.3/panTro3
Human           Homo sapiens            Feb. 2009   GRCh37/hg19
Gibbon          Nomascus leucogenys     Jan. 2010   GGSC Nleu1.0/nomLeu1
Orangutan       Pongo pygmaeus abelii   Jul. 2007   WUGSC 2.0.2/ponAbe2
Baboon          Papio hamadryas         Nov. 2008   Baylor 1.0/papHam1
Rhesus          Macaca mulatta          Jan. 2006   MGSC Merged 1.0/rheMac2
Marmoset        Callithrix jacchus      Mar. 2009   WUGSC 3.2/calJac3
Tarsier         Tarsius syrichta        Aug. 2008   Broad/tarSyr1
Mouse lemur     Microcebus murinus      Jun. 2003   Broad/micMur1
Bushbaby        Otolemur garnettii      Dec. 2006   Broad/otoGar1

---------------------------------------------------------------
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/gorGor3/phastCons11way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/gorGor3/phastCons11way

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.txt08-Dec-2011 10:28 3.5K 
[   ]phastCons11way.bw06-Dec-2011 16:17 7.0G 
[   ]phastCons11way.wigFix.gz06-Dec-2011 15:38 3.4G 
[SND]primate.mod06-Dec-2011 14:05 647  

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