This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/galVar1/phyloP5way/README.txt

This directory contains conversation scoring by phyloP (phylogenetic p-values)
from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple
alignments of 4 genomes to the Guinea pig genome.

Files in this directory are:

    galVar1.phyloP5way.mod  phyloP tree model with branch lengths
                        for the 5 genomes
    galVar1.phyloP5way.wigFix.gz - phyloP scores for the 5 genomes
                                 in fixed step wiggle format
    galVar1.phyloP5way.bw - phyloP scores for the 5 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/galVar1/multiz5way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=galVar1&g=cons5way

For a description of the phyloP wigFix 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:

Malayan flying lemur Galeopterus variegatus   Jun. 2014 (G_variegatus-3.0.2/galVar1) reference

Guinea pig         Cavia porcellus          Feb. 2008 (Broad/cavPor3) reference
Mouse              Mus musculus             Dec. 2011 (GRCm38/mm10)
Human              Homo sapiens             Dec. 2013 (GRCh38/hg38)
Tree shrew         Tupaia belangeri         Dec. 2006 (Broad/tupBel1)

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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 113 Mb of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/galVar1/phyloP5way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/galVar1/phyloP5way

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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