This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/dm6/phyloP124way/README.txt

This directory contains conservation scoring by phyloP (phylogenetic p-values)
from the PHAST package (http://compgen.cshl.edu/phast/) for multiple
alignments of 123 genome sequences to the reference assembly:
    D. melanogaster/dm6/Aug. 2014

See also: assemblyInformation.txt for information about which
          assemblies have been used in this 124-way multiple alignment

Files in this directory:

    dm6.124way.phyloP/*.wigFix.gz - scores in fixed step wiggle format
    dm6.phyloP124way.mod - phyloP tree model with branch lengths for
                            all 124 species
    dm6.phyloP124way.bw - scores in bigWig format
    md5sum.txt - MD5 checksums to verify download files
    nameCrossReference.txt - tab separated columns with the different names
                           - for these sequences and databases, columns:
                       1. sequence name - UCSC database or scientific name
                                        - sequence names used in MAF files
                       2. NCBI accession
                       3. NCBI taxon identifier
                       4. assembly name
                       5. scientific name
    assemblyInformation.txt - summary listing of each sequence used

See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
   for bigWig format description

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

The phastCons data can be found at:
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/phastCons124way/

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/multiz124way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=dm6&g=cons124way

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Note, the uncompressed *.wigFix.gz files are 741 Mb of data, when compressed, 
they are approximately 258 Mb of compressed data.  The entire set of
data in this directory is approximately 706 Mb.

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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/dm6/phyloP124way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/dm6/phyloP124way

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.

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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.

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References for phastCons and phyloP:

Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates
on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21.
(http://genome.cshlp.org/content/20/1/110.long)

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://genome.cshlp.org/content/15/8/1034.full)

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