This file is from:

    http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/phyloP44way/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 44 coronavirus sequences.

Files in this directory:

  md5sum.txt - md5 sums to verify copied files
  wuhCor1.44way.nameList.txt - relating the accession name to
                              sequence name, and sample collection date
  wuhCor1.phyloP44way.mod - phyloP tree model with branch lengths for
                             all 44 sequences
  wuhCor1.phyloP44way.bw - scores in bigWig format
  wuhCor1.phyloP44way.wigFix.gz - scores in fixed step wiggle format

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.soe.ucsc.edu/goldenPath/wuhCor1/phastCons44way/

The multiple alignments and methods description are at:
http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/multiz44way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=wuhCor1&g=cons44way

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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.soe.ucsc.edu/goldenPath/wuhCor1/phyloP44way/ ./

      OR

    ftp hgdownload.soe.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/wuhCor1/phyloP44way

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)

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