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.
---------------------------------------------------------------
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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Name Last modified Size Description
Parent Directory -
wuhCor1.phyloP44way.wigFix.gz 2020-03-13 21:25 45K
wuhCor1.phyloP44way.mod 2020-03-13 21:24 1.7K
wuhCor1.phyloP44way.bw 2020-03-13 21:25 122K
wuhCor1.44way.nameList.txt 2020-03-14 13:55 1.9K
md5sum.txt 2020-03-18 11:33 285