This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons4way/README.txt

This directory contains compressed phastCons scores for multiple alignments
of 3 genomes to the mouse genome (mm10, Dec. 2011):

Files in this directory are:
    mm10.phastCons4way.mod  phastCons tree model with branch lengths
                        for the 4 species
    mm10.phastCons4way.wigFix.gz - phastCons scores for the 4 species
                        in fixed step wiggle format
    mm10.phastCons4way.bw - phastCons scores for all 4 species
                        in bigWig format
    md5sum.txt - md5 sums of the files here to verify accurate download

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/mm10/multiz4way/

For a description of the wigFix data file format, note the section
describing the 'fixedStep' wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html

For a description of the phastCons data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
see also the section describing the 'fixedStep' wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html

Assemblies used in these alignments:

Mouse              Mus musculus             Dec. 2011 (GRCm38/mm10)  reference

Malayan flying lemur Galeopterus variegatus Jun. 2014 (WashU/galVar1)
Human              Homo sapiens             Dec. 2013 (GRCh38/hg38)
Chinese tree shrew Tupaia chinensis         Jan. 2013 (BGI TupChi1_1.0/tupChi1)

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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.
There is approximately 4.3 Gb of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons4way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/mm10/phastCons4way

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. 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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      Name                         Last modified      Size  Description
      Parent Directory                                  -   
      md5sum.txt                   2017-04-21 21:03  176   
      mm10.phastCons4way.bw        2017-04-21 00:47  2.9G  
      mm10.phastCons4way.wigFix.gz 2017-04-21 00:18  1.4G  
      mm10.phastCons4way.mod       2017-04-20 23:16  422