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
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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: <your email address>
go to the directory goldenPath/galGal6/multiz77way
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 usable for any
purpose. For data use restrictions regarding the individual
genome assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.
Name Last modified Size Description
Parent Directory -
upstream1000.ncbiRefSeq.maf.gz 2018-12-14 16:20 582M
upstream2000.ncbiRefSeq.maf.gz 2018-12-14 17:35 1.2G
upstream5000.ncbiRefSeq.maf.gz 2018-12-14 19:16 3.2G
alignments/ 2018-12-18 13:55 -
galGal6.77way.nh 2018-12-19 10:35 3.0K
galGal6.77way.scientificNames.nh 2018-12-19 10:37 3.7K
maf/ 2018-12-19 10:44 -
galGal6.77way.commonNames.nh 2019-09-11 12:14 3.4K