This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/phyloP27way/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 26 genomes to the D. melanogaster genome.
Files in this directory:
dm6.phyloP27way.mod - phyloP tree model with branch lengths for
all 27 species
dm6.phyloP27way.bw - scores in bigWig format
dm6.phyloP27way.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.cse.ucsc.edu/goldenPath/dm6/phastCons27way/
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/multiz27way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=dm6&g=cons27way
Assemblies used in these alignments: (alignment
type)
D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) reference
D. simulans Apr. 2005 (WUGSC 1.0/droSim1) syntenic
D. sechellia Oct. 2005 (Broad/droSec1) syntenic
D. yakuba Jun. 2006 (Flybase dyak_caf1/droYak3) syntenic
D. erecta Feb. 2006 (Agencourt CAF1/droEre2) syntenic
D. biarmipes Mar. 2013 (BCM Dbia_2.0/droBia2) syntenic
D. suzukii Sep. 2013 (BGI Dsuzukii.v01/droSuz1) syntenic
D. ananassae Feb. 2006 (Agencourt CAF1/droAna3) syntenic
D. bipectinata Mar. 2013 (BCM Dbip_2.0/droBip2) syntenic
D. eugracilis Mar. 2013 (modENCODE Deug_2.0/droEug2) syntenic
D. elegans Mar. 2013 (BCM Dele_2.0/droEle2) syntenic
D. kikkawai Mar. 2013 (BCM Dkik_2.0/droKik2) syntenic
D. takahashii Mar. 2013 (BCM Dtak_2.0/droTak2) syntenic
D. rhopaloa Feb. 2013 (modENCODE Drho_2.0/droRho2) syntenic
D. ficusphila Mar. 2013 (BCM Dfic_2.0/droFic2) syntenic
D. pseudoobscura Apr. 2013 (BCM Dpse_3.0/droPse3) syntenic
D. persimilis Oct. 2005 (Broad/droPer1) syntenic
D. miranda Apr. 2013 (U.C. Berkeley DroMir_2.2/droMir2) syntenic
D. willistoni Aug. 2006 (JCVI dwil_caf1/droWil2) syntenic
D. virilis Feb. 2006 (Agencourt CAF1/droVir3) syntenic
D. mojavensis Feb. 2006 (Agencourt CAF1/droMoj3) syntenic
D. albomicans May. 2012 (Kunming DroAlb_1.0/droAlb1) syntenic
D. grimshawi Feb. 2006 (Agencourt CAF1/droGri2) syntenic
Musca domestica Apr. 2013 (Glossina M_domestica-2.0.2/musDom2) net
Anopheles gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) net
Apis mellifera Nov. 2010 (BCM Amel_4.5/apiMel4) net
Tribolium castaneum Sep. 2005 (BCM 2.0/triCas2) net
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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/phyloP27way/ ./
OR
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/dm6/phyloP227way
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. 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 -
md5sum.txt 2014-12-05 14:36 167
dm6.phyloP27way.bw 2014-12-05 14:23 396M
dm6.phyloP27way.wigFix.gz 2014-12-05 14:19 225M
dm6.phyloP27way.mod 2014-11-13 15:29 1.0K