This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/regenRn1/phyloP7way/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 6 genomes to the rat/regenRn1/May 2019 genome.

Files in this directory are:

    regenRn1.phyloP7way.mod  phyloP tree model with branch lengths
                        for all the sequences
    regenRn1.7way.phyloP/*.wigFix.gz - phyloP scores for all the alignments
                                 in fixed step wiggle format
    regenRn1.phyloP7way.bw - phyloP scores for all the alignments
                          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/regenRn1/multiz7way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=regenRn1&g=cons7way

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:

Rat     Rattus norvegicus       May. 2019 (Regen Rn1/regenRn1)  (reference)

Mouse   Mus musculus            Dec. 2011 (GRCm38/mm10) (syntenic)
Rabbit  Oryctolagus cuniculus   Apr. 2009 (Broad/oryCun2) (syntenic)
Human   Homo sapiens            Dec. 2013 (GRCh38/hg38) (syntenic)
Crab-eating macaque     Macaca fascicularis
    Jun. 2013 (Macaca_fascicularis_5.0/macFas5) (syntenic)
Pig     Sus scrofa              Feb. 2017 (Sscrofa11.1/susScr11) (syntenic)
Dog     Canis lupus familiaris  Sep. 2011 (Broad CanFam3.1/canFam3) (syntenic)

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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 5.4 Gb of compressed data in this directory,
approximately 14 Gb uncompressed..

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/regenRn1/phyloP7way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/regenRn1/phyloP7way

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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