This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/phastCons7way/README.txt
This directory contains compressed phastCons scores for multiple alignments
of 6 vertebrate genomes to the medium ground finch genome, plus two alternate
set of scores for subsets of species in the alignments.
Files in this directory are:
geoFor1.7way.phastCons.mod - phastCons tree model for the 7 species
geoFor1.7way.phastCons.birds.mod - phastCons tree model for the birds subset:
geoFor1 taeGut1 melUnd1 galGal4 melGal1
(medium ground finch, zebra finch, budgerigar, chicken, turkey)
geoFor1.7way.phastCons.vertebrate.mod - tree model for vertebrate subset:
geoFor1 hg19 mm10
(medium ground finch, human, mouse)
Note, geoFor1 is included in each subset since it is the reference species.
phastCons scores in bigWig format files:
geoFor1.7way.phastCons.bw - all 7 species
geoFor1.7way.phastCons7wayBirds.bw - birds subset
geoFor1.7way.phastCons7wayVertebrate.bw - vertebrate subset
See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
for bigWig format description
phastCons scores in fixed step wiggle format files:
geoFor1.7way.phastCons/phastCons7way.wigFix.gz - scores for 7 species
birds/phastCons7way.birds.wigFix.gz - scores for the birds subset
vertebrate/phastCons7way.vertebrate.wigFix.gz - scores for the vertebrate subset
For a description of the phastCons fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
The phyloP data can be found at:
http://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/phyloP7way/
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/multiz7way/
Assemblies used in these alignments:
==== reference assembly:
Medium ground finch - Geospiza fortis Apr. 2012 BGI/geoFor1 reference
==== Birds subset:
Zebra finch Taeniopygia guttata Jul. 2008 WUGSC 3.2.4/taeGut1 Syntenic net
Budgerigar Melopsittacus undulatus Sep. 2011 WUSTL v6.3/melUnd1 Syntenic net
Chicken Gallus gallus Nov. 2011 ICGSC 4.0/galGal4 Syntenic net
Turkey Meleagris gallopavo Dec. 2009 TGC 2.01/melGal1 Syntenic net
==== Vertebrate subset:
Human Homo sapiens Feb. 2009 GRCh37/hg19 Reciprocal best
Mouse Mus musculus Dec. 2019 GRCm38/mm10 Reciprocal best
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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 8.5 Gb of compressed data in this directory.
Via rsync:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/phastCons7way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/geoFor1/phastCons7way
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. 2009 Oct 26. [Epub ahead of print]
(http://genome.cshlp.org/content/early/2009/10/26/gr.097857.109.abstract)
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://www.genome.org/cgi/doi/10.1101/gr.3715005)
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Name Last modified Size Description
Parent Directory -
geoFor1.7way.phastCons.mod 2012-08-03 09:38 510
geoFor1.7way.phastCons.birds.mod 2012-08-03 09:42 461
geoFor1.7way.phastCons.vertebrate.mod 2012-08-03 09:42 393
geoFor1.7way.phastCons.bw 2012-08-03 14:14 2.0G
geoFor1.7way.phastCons7wayBirds.bw 2012-08-06 09:53 2.0G
geoFor1.7way.phastCons7wayVertebrate.bw 2012-08-06 16:51 498M
birds/ 2012-08-16 15:21 -
vertebrate/ 2012-08-16 15:27 -
geoFor1.7way.phastCons/ 2012-08-16 15:30 -