This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/phyloP7way/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 6 vertebrate genomes to the medium ground finch genome,
plus two alternate sets of scores for subsets of species in the alignments.
Files in this directory are:
geoFor1.phyloP.7way.mod - phyloP tree model with branch lengths for
all 7 species
geoFor1.phyloP.birds.mod - tree model for the birds subset:
geoFor1 taeGut1 melUnd1 galGal4 melGal1
(medium ground finch, zebra finch, budgerigar, chicken, turkey)
geoFor1.phyloP.vertebrate.mod - tree model for the vertebrate subset:
geoFor1 hg19 mm10
(medium ground finch, human, mouse)
Note, geoFor1 is included in each subset since it is the reference species.
PhyloP scores in bigWig format files:
geoFor1.7way.phyloP7way.bw
geoFor1.7way.phyloP7wayBirds.bw
geoFor1.7way.phyloP7wayVertebrate.bw
See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
for bigWig format description
PhyloP scores in fixed step wiggle format:
geoFor1.7way.phyloP7way/phyloP7way.wigFix.gz - scores for all 7 species
birds/phyloP7way.birds.wigFix.gz - scores for the birds subset
vertebrate/phyloP7way.vertebrate.wigFix.gz - scores for the vertebrate subset
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/geoFor1/phastCons7way/
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/multiz7way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=geoFor1&g=cons7way
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:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/phyloP7way/ ./
OR
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/geoFor1/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.
---------------------------------------------------------------
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. 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 -
birds/ 2012-08-16 15:36 -
geoFor1.7way.phyloP.birds.mod 2012-08-06 08:48 431
geoFor1.7way.phyloP.vertebrate.mod 2012-08-03 15:22 363
geoFor1.7way.phyloP7way.bw 2012-08-03 15:45 2.0G
geoFor1.7way.phyloP7way.mod 2012-08-03 14:24 480
geoFor1.7way.phyloP7way/ 2012-08-16 15:46 -
geoFor1.7way.phyloP7wayBirds.bw 2012-08-06 09:37 1.9G
geoFor1.7way.phyloP7wayVertebrate.bw 2012-08-06 08:52 578M
md5sum.txt 2012-08-07 10:01 393
vertebrate/ 2012-08-16 15:41 -