This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz100way/README.txt
This directory contains compressed multiple alignments of the following
assemblies to the human genome (hg38/GRCh38, Dec. 2013):
Assemblies used in these alignments:
== Primate subset ==
Human Homo sapiens Dec 2013 GRCh38/hg38 Reference species
Chimp Pan troglodytes Feb 2011 CSAC 2.1.4/panTro4 Syntenic net
Gorilla Gorilla gorilla gorilla May 2011 gorGor3.1/gorGor3 Reciprocal best net
Orangutan Pongo pygmaeus abelii July 2007 WUGSC 2.0.2/ponAbe2 Reciprocal best net
Gibbon Nomascus leucogenys Oct 2012 GGSC Nleu3.0/nomLeu3 Syntenic net
Rhesus Macaca mulatta Oct 2010 BGI CR_1.0/rheMac3 Syntenic net
Crab-eating macaque Macaca fascicularis Jun 2013 Macaca_fascicularis_5.0/macFas5 Syntenic net
Baboon Papio hamadryas Mar 2012 Baylor Panu_2.0/papAnu2 Reciprocal best net
Green monkey Chlorocebus sabaeus Mar 2014 Chlorocebus_sabeus 1.1/chlSab2 Syntenic net
Marmoset Callithrix jacchus Mar 2009 WUGSC 3.2/calJac3 Syntenic net
Squirrel monkey Saimiri boliviensis Oct 2011 Broad/saiBol1 Syntenic net
Bushbaby Otolemur garnettii Mar 2011 Broad/otoGar3 Syntenic net
== Euarchontoglires subset ==
Chinese tree shrew Tupaia chinensis Jan 2013 TupChi_1.0/tupChi1 Syntenic net
Squirrel Spermophilus tridecemlineatus Nov 2011 Broad/speTri2 Syntenic net
Lesser Egyptian jerboa Jaculus jaculus May 2012 JacJac1.0/jacJac1 Syntenic net
Prairie vole Microtus ochrogaster Oct 2012 MicOch1.0/micOch1 Syntenic net
Chinese hamster Cricetulus griseus Jul 2013 C_griseus_v1.0/criGri1 Syntenic net
Golden hamster Mesocricetus auratus Mar 2013 MesAur1.0/mesAur1 Syntenic net
Mouse Mus musculus Dec 2011 GRCm38/mm10 Syntenic net
Rat Rattus norvegicus Jul 2014 RGSC 6.0/rn6 Syntenic net
Naked mole-rat Heterocephalus glaber Jan 2012 Broad HetGla_female_1.0/hetGla2 Syntenic net
Guinea pig Cavia porcellus Feb 2008 Broad/cavPor3 Syntenic net
Chinchilla Chinchilla lanigera May 2012 ChiLan1.0/chiLan1 Syntenic net
Brush-tailed rat Octodon degus Apr 2012 OctDeg1.0/octDeg1 Syntenic net
Rabbit Oryctolagus cuniculus Apr 2009 Broad/oryCun2 Syntenic net
Pika Ochotona princeps May 2012 OchPri3.0/ochPri3 Syntenic net
== Laurasiatheria subset ==
Pig Sus scrofa Aug 2011 SGSC Sscrofa10.2/susScr3 Syntenic net
Alpaca Vicugna pacos Mar 2013 Vicugna_pacos-2.0.1/vicPac2 Syntenic net
Bactrian camel Camelus ferus Dec 2011 CB1/camFer1 Syntenic net
Dolphin Tursiops truncatus Oct 2011 Baylor Ttru_1.4/turTru2 Reciprocal best net
Killer whale Orcinus orca Jan 2013 Oorc_1.1/orcOrc1 Syntenic net
Tibetan antelope Pantholops hodgsonii May 2013 PHO1.0/panHod1 Syntenic net
Cow Bos taurus Jun 2014 UMD_3.1.1/bosTau8 Syntenic net
Sheep Ovis aries Aug 2012 ISGC Oar_v3.1/oviAri3 Syntenic net
Domestic goat Capra hircus May 2012 CHIR_1.0/capHir1 Syntenic net
Horse Equus caballus Sep 2007 Broad/equCab2 Syntenic net
White rhinoceros Ceratotherium simum May 2012 CerSimSim1.0/cerSim1 Syntenic net
Cat Felis catus Nov 2014 ICGSC Felis_catus 8.0/felCat8 Syntenic net
Dog Canis lupus familiaris Sep 2011 Broad CanFam3.1/canFam3 Syntenic net
Ferret Mustela putorius furo Apr 2011 MusPutFur1.0/musFur1 Syntenic net
Panda Ailuropoda melanoleuca Dec 2009 BGI-Shenzhen 1.0/ailMel1 Syntenic net
Pacific walrus Odobenus rosmarus divergens Jan 2013 Oros_1.0/odoRosDiv1 Syntenic net
Weddell seal Leptonychotes weddellii Mar 2013 LepWed1.0/lepWed1 Reciprocal best net
Black flying-fox Pteropus alecto Aug 2012 ASM32557v1/pteAle1 Syntenic net
Megabat Pteropus vampyrus Jul 2008 Broad/pteVam1 Reciprocal best net
David's myotis bat Myotis davidii Aug 2012 ASM32734v1/myoDav1 Syntenic net
Microbat Myotis lucifugus Jul 2010 Broad Institute Myoluc2.0/myoLuc2 Syntenic net
Big brown bat Eptesicus fuscus Jul 2012 EptFus1.0/eptFus1 Syntenic net
Hedgehog Erinaceus europaeus May 2012 EriEur2.0/eriEur2 Syntenic net
Shrew Sorex araneus Aug 2008 Broad/sorAra2 Syntenic net
Star-nosed mole Condylura cristata Mar 2012 ConCri1.0/conCri1 Syntenic net
== Afrotheria subset ==
Elephant Loxodonta africana Jul 2009 Broad/loxAfr3 Syntenic net
Cape elephant shrew Elephantulus edwardii Aug 2012 EleEdw1.0/eleEdw1 Syntenic net
Manatee Trichechus manatus latirostris Oct 2011 Broad v1.0/triMan1 Syntenic net
Cape golden mole Chrysochloris asiatica Aug 2012 ChrAsi1.0/chrAsi1 Syntenic net
Tenrec Echinops telfairi Nov 2012 Broad/echTel2 Syntenic net
Aardvark Orycteropus afer afer May 2012 OryAfe1.0/oryAfe1 Syntenic net
== Mammal subset ==
Armadillo Dasypus novemcinctus Dec 2011 Baylor/dasNov3 Syntenic net
Opossum Monodelphis domestica Oct 2006 Broad/monDom5 Net
Tasmanian devil Sarcophilus harrisii Feb 2011 WTSI Devil_ref v7.0/sarHar1 Net
Wallaby Macropus eugenii Sep 2009 TWGS Meug_1.1/macEug2 Reciprocal best net
Platypus Ornithorhynchus anatinus Mar 2007 WUGSC 5.0.1/ornAna1 Reciprocal best net
== Aves subset ==
Saker falcon Falco cherrug Feb 2013 F_cherrug_v1.0/falChe1 Net
Peregrine falcon Falco peregrinus Feb 2013 F_peregrinus_v1.0/falPer1 Net
Collared flycatcher Ficedula albicollis Jun 2013 FicAlb1.5/ficAlb2 Net
White-throated sparrow Zonotrichia albicollis Apr 2013 ASM38545v1/zonAlb1 Net
Medium ground finch Geospiza fortis Apr 2012 GeoFor_1.0/geoFor1 Net
Zebra finch Taeniopygia guttata Feb 2013 WashU taeGut324/taeGut2 Net
Tibetan ground jay Pseudopodoces humilis Jan 2013 PseHum1.0/pseHum1 Net
Budgerigar Melopsittacus undulatus Sep 2011 WUSTL v6.3/melUnd1 Net
Parrot Amazona vittata Jan 2013 AV1/amaVit1 Net
Scarlet macaw Ara macao Jun 2013 SMACv1.1/araMac1 Net
Rock pigeon Columba livia Feb 2013 Cliv_1.0/colLiv1 Net
Mallard duck Anas platyrhynchos Apr 2013 BGI_duck_1.0/anaPla1 Net
Chicken Gallus gallus Nov 2011 ICGSC Gallus_gallus-4.0/galGal4 Net
Turkey Meleagris gallopavo Dec 2009 TGC Turkey_2.01/melGal1 Net
== Sarcopterygii subset ==
American alligator Alligator mississippiensis Aug 2012 allMis0.2/allMis1 Net
Green seaturtle Chelonia mydas Mar 2013 CheMyd_1.0/cheMyd1 Net
Painted turtle Chrysemys picta bellii Mar 2014 v3.0.3/chrPic2 Net
Chinese softshell turtle Pelodiscus sinensis Oct 2011 PelSin_1.0/pelSin1 Net
Spiny softshell turtle Apalone spinifera May 2013 ASM38561v1/apaSpi1 Net
Lizard Anolis carolinensis May 2010 Broad AnoCar2.0/anoCar2 Net
X. tropicalis Xenopus tropicalis Sep 2012 JGI 7.0/xenTro7 Net
Coelacanth Latimeria chalumnae Aug 2011 Broad/latCha1 Net
== Fish subset ==
Tetraodon Tetraodon nigroviridis Mar 2007 Genoscope 8.0/tetNig2 Net
Fugu Takifugu rubripes Oct 2011 FUGU5/fr3 Net
Yellowbelly pufferfish Takifugu flavidus May 2013 version 1 of Takifugu flavidus genome/takFla1 Net
Nile tilapia Oreochromis niloticus Jan 2011 Broad oreNil1.1/oreNil2 Net
Princess of Burundi Neolamprologus brichardi May 2011 NeoBri1.0/neoBri1 Net
Burton's mouthbreeder Haplochromis burtoni Oct 2011 AstBur1.0/hapBur1 Net
Zebra mbuna Maylandia zebra Mar 2012 MetZeb1.1/mayZeb1 Net
Pundamilia nyererei Pundamilia nyererei Oct 2011 PunNye1.0/punNye1 Net
Medaka Oryzias latipes Oct 2005 NIG/UT MEDAKA1/oryLat2 Net
Southern platyfish Xiphophorus maculatus Jan 2012 Xiphophorus_maculatus-4.4.2/xipMac1 Net
Stickleback Gasterosteus aculeatus Feb 2006 Broad/gasAcu1 Net
Atlantic cod Gadus morhua May 2010 Genofisk GadMor_May2010/gadMor1 Net
Zebrafish Danio rerio Sep 2014 Zv10/danRer10 Net
Mexican tetra (cavefish) Astyanax mexicanus Apr 2013 Astyanax_mexicanus-1.0.2/astMex1 Net
Spotted gar Lepisosteus oculatus Dec 2011 LepOcu1/lepOcu1 Net
Lamprey Petromyzon marinus Sep 2010 WUGSC 7.0/petMar2 Net
---------------------------------------------------------------
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons100way
based on the phylogenetic tree: hg38.100way.nh.
Files in this directory:
- hg38.100way.nh - phylogenetic tree used during the multiz multiple alignment
- hg38.100way.commonNames.nh - same as hg38.100way.nh with the UCSC database
name replaced by the common name for the species
- hg38.100way.scientificNames.nh - same as hg38.100way.nh with the UCSC
database name replaced by the scientific name for the species
See also:
http://genomewiki.ucsc.edu/index.php/Hg38_100way_conservation_alignment
The "alignments" directory contains compressed FASTA alignments
for the UCSC Known Gene CDS regions of the human genome (hg38/GRCh38, Feb. 2009)
aligned to the assemblies.
The maf/chr*.maf.gz files each contain all the alignments to that particular
human chromosome, with additional annotations to indicate gap context, and
genomic breaks for the sequence in the underlying genome assemblies. Beware,
the compressed data size of these files is about 70 Gb, uncompressed
size is about 730 Gb.
The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for UCSC Known 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
human, 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 human; 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. These files
are updated weekly.
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/hg38/phastCons100way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP100way
---------------------------------------------------------------
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 31 Gb of compressed data in this directory.
Via rsync:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz100way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/hg38/multiz100way
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 -
upstream5000.knownGene.maf.gz 2015-05-11 19:30 3.5G
upstream2000.knownGene.maf.gz 2015-05-11 17:26 1.6G
upstream1000.knownGene.maf.gz 2015-05-11 15:18 953M
md5sum.txt 2017-10-06 10:39 367
maf/ 2015-05-12 09:12 -
hg38.100way.scientificNames.nh 2015-02-06 13:55 4.2K
hg38.100way.nh 2015-05-11 12:46 3.4K
hg38.100way.commonNames.nh 2016-01-11 09:20 3.6K
alignments/ 2022-11-09 14:11 -