This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/fr3/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 fish genomes to the Fugu genome.

Files in this directory are:
    fish.mod - phyloP tree model with branch lengths for all 8 species:
                        fugu, tetraodon, nile tilapia, stickleback, medaka,
                        atlantic cod, zebrafish, coelacanth)

    phyloP8way.wigFix.gz phyloP scores for all 8 species, wiggle fixed step
    phyloP8way.bw phyloP scores for all 8 species in bigWig format

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/fr3/multiz8way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=fr3&g=cons8way

Assemblies used in these alignments:

Fugu            Takifugu rubripes       Oct. 2011   FUGU5/fr3
Tetraodon       Tetraodon nigroviridis  Mar. 2007   Genoscope 8.0/tetNig2
Nile tilapia    Oreochromis niloticus   Jan. 2011   Broad/oreNil1
Stickleback     Gasterosteus aculeatus  Feb. 2006   Broad/gasAcu1
Atlantic cod    Gadus morhua            May. 2010   Genofisk/gadMor1
Medaka          Oryzias latipes         Oct. 2005   NIG/oryLat2
Zebrafish       Danio rerio             Jul. 2010   Zv9/danRer7
Coelacanth      Latimeria chalumnae     Aug. 2011   Broad/latCha1

---------------------------------------------------------------
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 1.8 Gb of compressed data in this directory.

   rsync -av --progress \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/phyloP8way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/fr3/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)