This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/galGal6/phyloP77way/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 76 genomes to the Gallus gallus/galGal6 chicken genome.
Files in this directory are:
galGal6.phyloP77way.mod phyloP tree model with branch lengths
for all the sequences
galGal6.77way.phyloP/*.wigFix.gz - phyloP scores for all the alignments
in fixed step wiggle format
galGal6.phyloP77way.bw - phyloP scores for all the alignments
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/galGal6/multiz77way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=galGal6&g=cons77way
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:
Chicken - Gallus gallus
Mar. 2018 (GRCg6a/galGal6) (reference)
Adelie penguin - Pygoscelis adeliae
Jun 2014 (ASM69910v1/pygAde1) (syntenic)
African clawed frog - Xenopus laevis
Aug. 2016 (Xenopus_laevis_v2/xenLae2) (net)
American alligator - Alligator mississippiensis
Aug. 2012 (allMis0.2/allMis1) (reciprocal best)
American crow - Corvus brachyrhynchos
Jun 2014 (ASM69197v1/corBra1) (syntenic)
American flamingo - Phoenicopterus ruber ruber
May 2014 (ASM68726v1/phoRub1) (reciprocal best)
Anna's hummingbird - Calypte anna
Jun 2014 (ASM69908v1/calAnn1) (syntenic)
Arctic lamprey - Lethenteron camtschaticum
Sep 2013 (LetJap1.0/letCam1) (net)
Bald eagle - Haliaeetus leucocephalus
Aug 2014 (Haliaeetus_leucocephalus-4.0/halLeu1) (syntenic)
Bar tailed trogon - Apaloderma vittatum
16 Jun 2014 (ASM70340v1/apaVit1) (reciprocal best)
Barn owl - Tyto alba
May 2014 (ASM68720v1/tytAlb1) (reciprocal best)
Brown roatelo - Mesitornis unicolor
Jun 2014 (ASM69576v1/mesUni1) (reciprocal best)
Budgerigar - Melopsittacus undulatus
Sep. 2011 (WUSTL v6.3/melUnd1) (syntenic)
Burmese python - Python bivittatus
Sep. 2013 (Python_molurus_bivittatus-5.0.2/pytBiv1) (net)
Canary - Serinus canaria
15 Jan-2014 (SCA1/serCan1) (syntenic)
Chinese alligator - Alligator sinensis
29 Aug 2013 (ASM45574v1/allSin1) (reciprocal best)
Chinese softshell turtle - Pelodiscus sinensis
Oct 2011 (PelSin_1.0/pelSin1) (reciprocal best)
Chuck-will's-widow - Caprimulgus carolinensis
Jun 2014 (ASM70074v1/capCar1) (reciprocal best)
Collared flycatcher - Ficedula albicollis
Jun 2013 (FicAlb1.5/ficAlb2) (syntenic)
Common cuckoo - Cuculus canorus
Jun 2014 (ASM70932v1/cucCan1) (reciprocal best)
Crested ibis - Nipponia nippon
Jun 2014 (ASM70822v1/nipNip1) (syntenic)
Crowned crain - Balearica pavonina gibbericeps
Jun 2014 (ASM70989v1/balPav1) (reciprocal best)
Cuckoo roller - Leptosomus discolor
May 2014 (ASM69178v1/lepDis1) (reciprocal best)
Dalmatian pelican - Pelecanus crispus
May 2014 (ASM68737v1/pelCri1) (reciprocal best)
Downy woodpecker - Picoides pubescens
Jun 2014 (ASM69900v1/picPub1) (reciprocal best)
Emperor penguin - Aptenodytes forsteri
06 Jun 2014 (ASM69914v1/aptFor1) (syntenic)
Fugu - Takifugu rubripes
Oct. 2011 (FUGU5/fr3) (net)
Garter snake - Thamnophis sirtalis
Jun. 2015 (Thamnophis_sirtalis-6.0/thaSir1) (net)
Golden eagle - Aquila chrysaetos canadensis
Oct. 2014 (aquChr-1.0.2/aquChr2) (syntenic)
Great cormorant - Phalacrocorax carbo
Jun 2014 (ASM70892v1/phaCar1) (reciprocal best)
Green seaturtle - Chelonia mydas
Mar 2013 (CheMyd_1.0/cheMyd1) (reciprocal best)
Hoatzin - Opisthocomus hoazin
May 2014 (ASM69207v1/opiHoa1) (reciprocal best)
Hooded crow - Corvus cornix cornix
Aug 2014 (Hooded_Crow_genome/corCor1) (syntenic)
Houbara bustard - Chlamydotis undulata macqueenii
Jun 2014 (ASM69519v1/chlUnd1) (reciprocal best)
Human - Homo sapiens
Dec. 2013 (GRCh38/hg38) (net)
Japanese eel - Anguilla japonica
18 Mar-2014 (japanese_eel_genome_v1_25_oct_2011_japonica_c401b400k25m200_sspacepremiumk3a02n24_extra.final.scaffolds/angJap1) (net)
Japanese quail - Coturnix japonica
Mar. 2016 (Coturnix japonica 2.0/cotJap2) (reciprocal best)
Killdeer - Charadrius vociferus
Aug 2014 (ASM70802v2/chaVoc2) (syntenic)
Lamprey - Petromyzon marinus
Dec. 2017 (Pmar_germline 1.0/petMar3) (net)
Little egret - Egretta garzetta
May 2014 (ASM68718v1/egrGar1) (reciprocal best)
Lizard - Anolis carolinensis
May 2010 (Broad AnoCar2.0/anoCar2) (net)
Mallard duck - Anas platyrhynchos
Apr 2013 (BGI_duck_1.0/anaPla1) (reciprocal best)
Medaka - Oryzias latipes
Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (net)
Medium ground finch - Geospiza fortis
Apr. 2012 (GeoFor_1.0/geoFor1) (syntenic)
Mouse - Mus musculus
Dec. 2011 (GRCm38/mm10) (net)
Nile tilapia - Oreochromis niloticus
Nov. 2016 (ASM185804v2/oreNil3) (net)
Northern carmine bee-eater - Merops nubicus
May 2014 (ASM69184v1/merNub1) (reciprocal best)
Northern fulmar - Fulmarus glacialis
May 2014 (ASM69083v1/fulGla1) (reciprocal best)
Ostrich - Struthio camelus australis
06 Jun-2014 (ASM69896v1/strCam1) (reciprocal best)
Painted turtle - Chrysemys picta bellii
Mar. 2014 (v3.0.3/chrPic2) (syntenic)
Parrot - Amazona vittata
Jan. 2013 (AV1/amaVit1) (reciprocal best)
Peregrine falcon - Falco peregrinus
Feb 2013 (F_peregrinus_v1.0/falPer1) (syntenic)
Red crested turaco - Tauraco erythrolophus
Jun 2014 (ASM70936v1/tauEry1) (reciprocal best)
Red-legged seriema - Cariama cristata
May 2014 (ASM69053v1/carCri1) (reciprocal best)
Red-throated loon - Gavia stellata
May 2014 (ASM69087v1/gavSte1) (reciprocal best)
Rhinoceros hornbill - Buceros rhinoceros silvestris
Jun 2014 (ASM71030v1/bucRhi1) (reciprocal best)
Rifleman - Acanthisitta chloris
27 May 2014 (ASM69581v1/acaChl1) (reciprocal best)
Rock pigeon - Columba livia
Feb 2013 (Cliv_1.0/colLiv1) (syntenic)
Saker falcon - Falco cherrug
Feb 2013 (F_cherrug_v1.0/falChe1) (syntenic)
Scarlet macaw - Ara macao
Jun 2013 (SMACv1.1/araMac1) (reciprocal best)
Speckled mousebird - Colius striatus
May 2014 (ASM69071v1/colStr1) (reciprocal best)
Spiny softshell turtle - Apalone spinifera
May 2013 (ASM38561v1/apaSpi1) (reciprocal best)
Stickleback - Gasterosteus aculeatus
Feb. 2006 (Broad/gasAcu1) (net)
Sunbittern - Eurypyga helias
May 2014 (ASM69077v1/eurHel1) (reciprocal best)
Tetraodon - Tetraodon nigroviridis
Mar. 2007 (Genoscope 8.0/tetNig2) (net)
Tibetan frog - Nanorana parkeri
Mar. 2015 (BGI_ZX_2015/nanPar1) (net)
Tibetan ground jay - Pseudopodoces humilis
Jan 2013 (PseHum1.0/pseHum1) (syntenic)
Turkey - Meleagris gallopavo
Nov. 2014 (Turkey_5.0/melGal5) (reciprocal best)
White throated tinamou - Tinamus guttatus
Aug 2014 (ASM70537v2/tinGut2) (reciprocal best)
White-tailed eagle - Haliaeetus albicilla
May 2014 (ASM69140v1/halAlb1) (reciprocal best)
White-tailed tropicbird - Phaethon lepturus
May 2014 (ASM68728v1/phaLep1) (reciprocal best)
White-throated sparrow - Zonotrichia albicollis
Apr 2013 (ASM38545v1/zonAlb1) (syntenic)
X. tropicalis - Xenopus tropicalis
Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) (net)
Yellow-throated sandgrouse - Pterocles gutturalis
Jun 2014 (ASM69924v1/pteGut1) (reciprocal best)
Zebra finch - Taeniopygia guttata
Feb. 2013 (WashU taeGut324/taeGut2) (syntenic)
Zebra mbuna - Maylandia zebra
Mar 2012 (MetZeb1.1/mayZeb1) (net)
Zebrafish - Danio rerio
May 2017 (GRCz11/danRer11) (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.
There is approximately 5.8 Gb of compressed data in this directory,
approximately 10 Gb uncompressed..
Via rsync:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal6/phyloP77way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/galGal6/phyloP77way
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 2018-12-14 15:31 115
galGal6.phyloP77way.mod 2018-12-06 15:53 2.5K
galGal6.phyloP77way.bw 2018-12-07 08:20 3.7G
galGal6.77way.phyloP/ 2018-12-19 10:47 -