This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/ce11/phyloP26way/README.txt
This directory contains conversation scoring by phyloP (phylogenetic p-values)
from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple
alignments of 26 nematode genomes to the C. elegans genome.
Files in this directory are:
ce11.phyloP26way.mod phyloP tree model with branch lengths
for the 26 nematodes
ce11.phyloP26way.wigFix.gz - phyloP scores for the 26 nematodes
in fixed step wiggle format
ce11.phyloP26way.bw - phyloP scores for the 26 nematodes species
in bigWig format
md5sum.txt - md5 sums of the files here to verify accurate download
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/ce11/multiz26way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=ce11&g=cons26way
For a description of the phyloP wigFix data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
see also the section describing the 'fixedStep' wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html
Assemblies used in these alignments:
C. elegans Caenorhabditis elegans Feb. 2013 (WBcel235/ce11) reference
A. ceylanicum Ancylostoma ceylanicum Mar. 2014
(WS243/Acey_2013.11.30.genDNA/ancCey1)
Barber pole worm Haemonchus contortus Jul. 2013 (WormBase WS239/haeCon2)
C. angaria Caenorhabditis angaria Mar. 2012 (WS245/caeAng2)
C. brenneri Caenorhabditis brenneri Nov. 2010
(C. brenneri 6.0.1b/caePb3)
C. briggsae Caenorhabditis briggsae Apr. 2011 (WS225/cb4)
C. japonica Caenorhabditis japonica Aug. 2010 (WUSTL 7.0.1/caeJap4)
C. remanei Caenorhabditis remanei Jul. 2007 (WS220/caeRem4)
C. sp. 5 ju800 Caenorhabditis sp5 ju800 Jan. 2012
(WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51)
C. tropicalis Caenorhabditis tropicalis Nov. 2010 (WUSTL 3.0.1/caeSp111)
Dog heartworm Dirofilaria immitis Sep. 2013
(WS240/D. immitis v2.2/dirImm1)
Eye worm Loa loa Jul. 2012
(WS235/L_loa_Cameroon_isolate/loaLoa1)
Filarial worm Brugia malayi May. 2014
(WS244/B_malayi-3.1/bruMal2)
H. bacteriophora/m31e Heterorhabditis bacteriophora Aug. 2011
(WS229/H. bacteriophora 7.0/hetBac1)
M. hapla Meloidogyne hapla Sep. 2008
(M. hapla VW9 WS210/melHap1)
M. incognita Meloidogyne incognita Feb. 2008
(M. incognita WS245/PRJEA28837/melInc2)
Microworm Panagrellus redivivus Feb. 2013 (Pred3/panRed1)
N. americanus Necator americanus Dec. 2013
(WS242/N_americanus_v1/necAme1)
O. volvulus Onchocerca volvulus Nov. 2013
(WS241/O_volvulus_Cameroon_v3/oncVol1)
P. exspectatus Pristionchus exspectatus Mar. 2014
(WS243/P_exspectatus_v1/priExs1)
P. pacificus Pristionchus pacificus Aug. 2014 (P_pacificus-v2/priPac3)
Pig roundworm Ascaris suum Sep. 2012
(WS229/AscSuum_1.0/ascSuu1)
Pine wood nematode Bursaphelenchus xylophilus Nov. 2011
(WS229/B. xylophilus Ka4C1/burXyl1)
Threadworm Strongyloides ratti Sep. 2014 (S. ratti ED321/strRat2)
Trichinella Trichinella spiralis Jan. 2011
(WS225/Trichinella_spiralis-3.7.1/triSpi1)
Whipworm Trichuris suis Jul. 2014 (WS243/T. suis
DCEP-RM93M male/triSui1)
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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 113 Mb of compressed data in this directory.
Via rsync:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/ce11/phyloP26way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/ce11/phyloP26way
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.full)
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Name Last modified Size Description
Parent Directory -
md5sum.txt 2015-09-09 15:18 170
ce11.phyloP26way.bw 2015-09-08 12:42 172M
ce11.phyloP26way.wigFix.gz 2015-09-08 12:40 98M
ce11.phyloP26way.mod 2015-09-08 12:14 1.0K