This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/galGal6/multiz77way/README.txt This directory contains compressed multiple alignments of 76 genomes to the Gallus gallus/galGal6/March 2018 chicken genome. These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=galGal6&g=cons77way based on the phylogenetic tree: galGal6.77way.nh. Files in this directory: - galGal6.77way.nh - phylogenetic tree used during the multiz multiple alignment, using the UCSC database name, or sequence name for those sequences that are not hosted in UCSC databases. - galGal6.77way.scientificName.nh - same as galGal6.77way.nh with the sequence name replaced with the scientific name for the species. galGal6.77way.commonNames.nh - same as galGal6.77way.nh with the sequence name replaced with the common name - upstream*.ncbiRefSeq.maf.gz - alignments of regions upstream of NCBI RefSeq genes - maf/chr*.maf.gz - the multiple alignments on chicken for each chromosome - md5sum.txt - md5 check sums of these files to verify correct download files The "alignments" directory contains compressed FASTA alignments for the CDS regions for three gene tracks, ws245Genes, refGene, ensGene, of the chicken genome (galGal6, Mar. 2018) aligned to the assemblies. The maf/chr*.maf.gz files contain all the alignments for the chromosomes in the chicken genome, including additional annotations to indicate gap context and genomic breaks for the sequence in the underlying genome assemblies. Note, the compressed data size of these maf files is 35 Gb, uncompressed is approximately 335 Gb. The upstream*.ncbiRefSeq.maf.gz files contain alignments in regions upstream of annotated transcription starts for NCBI RefSeq genes. with annotated 5' UTRs. These files differ from the standard MAF format: they display alignments that extend from start to end of the upstream region in chicken, whether or not alignments actually exist. In situations where no alignments exist or the alignments of one or more species are missing, dot (".") is used as a placeholder. Multiple regions of an assembly's sequence may align to a single region in chicken; therefore, only the species name is displayed in the alignment data and no position information is recorded. The alignment score is always zero in these files. For a description of multiple alignment format (MAF), see http://genome.ucsc.edu/goldenPath/help/maf.html. PhastCons conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/galGal6/phastCons77way PhyloP conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/galGal6/phyloP77way --------------------------------------------------------------- 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 40 Gb of compressed data in this directory, approximately 340 Gb uncompressed. Via rsync: rsync -av --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal6/multiz77way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/galGal6/multiz77way 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 usable for any purpose. For data use restrictions regarding the individual genome assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.