This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/phyloP124way/README.txt
This directory contains conservation scoring by phyloP (phylogenetic p-values)
from the PHAST package (http://compgen.cshl.edu/phast/) for multiple
alignments of 123 genome sequences to the reference assembly:
D. melanogaster/dm6/Aug. 2014
See also: assemblyInformation.txt for information about which
assemblies have been used in this 124-way multiple alignment
Files in this directory:
dm6.124way.phyloP/*.wigFix.gz - scores in fixed step wiggle format
dm6.phyloP124way.mod - phyloP tree model with branch lengths for
all 124 species
dm6.phyloP124way.bw - scores in bigWig format
md5sum.txt - MD5 checksums to verify download files
nameCrossReference.txt - tab separated columns with the different names
- for these sequences and databases, columns:
1. sequence name - UCSC database or scientific name
- sequence names used in MAF files
2. NCBI accession
3. NCBI taxon identifier
4. assembly name
5. scientific name
assemblyInformation.txt - summary listing of each sequence used
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.cse.ucsc.edu/goldenPath/dm6/phastCons124way/
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/multiz124way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=dm6&g=cons124way
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Note, the uncompressed *.wigFix.gz files are 741 Mb of data, when compressed,
they are approximately 258 Mb of compressed data. The entire set of
data in this directory is approximately 706 Mb.
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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.cse.ucsc.edu/goldenPath/dm6/phyloP124way/ ./
OR
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/dm6/phyloP124way
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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Name Last modified Size Description
Parent Directory -
nameCrossReference.txt 2018-11-28 09:37 8.7K
dm6.124way.phyloP/ 2018-11-28 14:33 -
assemblyInformation.txt 2018-11-28 16:46 14K
dm6.phyloP124way.mod 2018-12-20 15:44 4.6K
dm6.phyloP124way.bw 2018-12-21 09:24 448M
md5sum.txt 2018-12-21 11:54 224