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) --------------------------------------------------------------- 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: go to the directory goldenPath/galGal6/phyloP77way To download multiple files from the UNIX command line, use the "mget" command. mget ... - 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) ---------------------------------------------------------------