This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/mm10/multiz60way/README.txt
This directory contains compressed multiple alignments of the following assemblies
to the mouse genome (mm10/GRCm38, Dec. 2011):
Assemblies used in these alignments:
==== Glire subset:
Mouse Mus musculus Dec. 2011 GRCm38/mm10 reference
Guinea pig Cavia porcellus Feb. 2008 Broad/cavPor3 Syntenic net
Kangaroo rat Dipodomys ordii Jul. 2008 Broad/dipOrd1 Reciprocal best
Naked mole-rat Heterocephalus glaber Jan. 2012
Broad HetGla_female_1.0/hetGla2 Syntenic net
Pika Ochotona princeps Jul. 2008 Broad/ochPri2 Reciprocal best
Rabbit Oryctolagus cuniculus Apr. 2009 Broad/oryCun2 Syntenic net
Rat Rattus norvegicus Mar. 2012 RGSC 5.0/rn5 Syntenic net
Squirrel Spermophilus
tridecemlineatus Nov. 2011 Broad/speTri2 Syntenic net
==== Euarchontoglire subset, includes the glire subset above plus:
Tree shrew Tupaia belangeri Dec. 2006 Broad/tupBel1 Reciprocal best
Marmoset Callithrix jacchus Mar. 2009 WUGSC 3.2/calJac3 Syntenic net
Gorilla Gorilla gorilla May. 2011 gorGor3 Syntenic net
Human Homo sapiens Feb. 2009 GRCh37/hg19 Syntenic net
Mouse lemur Microcebus murinus Jun. 2003 Broad/micMur1 Reciprocal best
Gibbon Nomascus leucogenys Jun. 2011 GGSC Nleu1.1/nomLeu2 Syntenic net
Bushbaby Otolemur garnettii Mar. 2011 Broad/otoGar3 Syntenic net
Chimp Pan troglodytes Feb. 2011
Pan_troglodytes-2.1.4/panTro4 Syntenic net
Baboon Papio hamadryas Nov. 2008 Baylor 1.0/papHam1 Reciprocal best
Orangutan Pongo pygmaeus abelii July 2007 WUGSC 2.0.2/ponAbe2 Syntenic net
Chinese rhesus Macaca mulatta Oct. 2010 BGI CR_1.0/rheMac3 Syntenic net
Squirrel monkey Saimiri boliviensis Oct. 2011 saiBol1 Syntenic net
Tarsier Tarsius syrichta Aug. 2008 Broad/tarSyr1 Reciprocal best
==== Placental subset, includes the glire and euarchontoglire subsets above plus:
Panda Ailuropoda melanoleuca Dec. 2009 BGI-Shenzhen 1.0/ailMel1 Syntenic Net
Cow Bos taurus Oct. 2011 Baylor Btau_4.6.1/bosTau7 Syntenic Net
Dog Canis lupus familiaris Sep. 2011 Broad/canFam3) Syntenic net
Sloth Choloepus hoffmanni Jul. 2008 Broad//choHof1 Reciprocal best
Armadillo Dasypus novemcinctus Dec. 2011 Armadillo/dasNov3 Reciprocal best
Tenrec Echinops telfairi Jul. 2005 Broad/echTel1 Reciprocal best
Horse Equus caballus Sep. 2007 Broad/equCab2 Syntenic net
Hedgehog Erinaceus europaeus Jun. 2006 Broad/eriEur1 Reciprocal best
Cat Felis catus Sep. 2011
ICGSC Felis_catus 6.2/felCat5 Reciprocal best
Elephant Loxodonta africana Jul. 2009 Broad/loxAfr3 Syntenic net
Microbat Myotis lucifugus Jul. 2010 Broad/myoLuc2 Reciprocal best
Sheep Ovis aries Feb. 2010 ISGC/oviAri1 Reciprocal best
Rock hyrax Procavia capensis Jul. 2008 Broad/proCap1 Reciprocal best
Megabat Pteropus vampyrus Jul. 2008 Broad/pteVam1 Reciprocal best
Shrew Sorex araneus Jun. 2006 Broad/sorAra1 Reciprocal best
Pig Sus scrofa Aug. 2011 SGSC Sscrofa10.2/susScr3 Syntenic net
Manatee Trichechus manatus latirostris Oct. 2011 Broad v1.0/triMan1 Syntenic net
Dolphin Tursiops truncatus Oct. 2011 Baylor Ttru_1.4/turTru2 Reciprocal best
Alpaca Vicugna pacos Jul. 2008 Broad/vicPac1 Reciprocal best
==== the rest of the vertebrates with the above complete the full 60-way species:
Lizard Anolis carolinensis May 2010 Broad/anoCar2 net
Painted turtle Chrysemys picta bellii Dec. 2011 v3.0.1/chrPic1 net
Zebrafish Danio rerio Jul. 2010 Zv9/danRer7 net
Fugu Takifugu rubripes Oct. 2011 FUGU5/fr3 net
Atlantic cod Gadus morhua May. 2010
Genofisk GadMor_May2010/gadMor1 net
Chicken Gallus gallus Nov. 2011
ICGSC Gallus_gallus-4.0/galGal4 net
Stickleback Gasterosteus aculeatus Feb. 2006 Broad/gasAcu1 net
Coelacanth Latimeria chalumnae Aug. 2011 latCha1 net
Wallaby Macropus eugenii Sep. 2009 TWGS Meug_1.1/macEug2 Reciprocal best
Turkey Meleagris gallopavo Dec. 2009 TGC Turkey_2.01/melGal1 net
Budgerigar Melopsittacus undulatus Sep. 2011 WUSTL v6.3/melUnd1 net
Opossum Monodelphis domestica Oct. 2006 Broad/monDom5 net
Nile tilapia Oreochromis niloticus Jan. 2011 Nile tilapia/oreNil2 net
Platypus Ornithorhynchus anatinus Mar. 2007 WUGSC 5.0.1/ornAna1 net
Medaka Oryzias latipes Oct. 2005 NIG/UT MEDAKA1/oryLat2 net
Lamprey Petromyzon marinus Mar. 2007 WUGSC 3.0/petMar1 net
Tasmanian devil Sarcophilus harrisii Feb. 2011
WTSI Devil_ref v7.0/sarHar1 net
Zebra finch Taeniopygia guttata Jul. 2008 WUGSC 3.2.4/taeGut1 net
Tetraodon Tetraodon nigroviridis Mar. 2007 Genoscope 8.0/tetNig2 net
X. tropicalis Xenopus tropicalis Nov. 2009 JGI 4.2/xenTro3 net
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=cons60way
based on the phylogenetic tree: mm10.60way.nh.
Files in this directory:
- mm10.60way.nh - phylogenetic tree used during the multiz multiple alignment
- mm10.commonNames.60way.nh - same as mm10.60way.nh with the UCSC database
name replaced by the common name for the species
See also:
http://genomewiki.ucsc.edu/index.php/Mm10_conservation_alignment
The "alignments" directory contains compressed FASTA alignments
for the RefSeq CDS regions of the mouse genome (mm10/GRCm38, Dec. 2011)
aligned to the assemblies.
The maf/chr*.maf.gz files each contain all the alignments to that particular
mouse 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 24 Gb.
The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for 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
mouse, 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 mouse; 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/mm10/phastCons60way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phyloP60way
---------------------------------------------------------------
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/mm10/multiz60way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/mm10/multiz60way
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 -
maf/ 2019-11-06 11:04 -
alignments/ 2019-10-11 12:04 -
md5sum.txt 2014-04-22 10:28 270
upstream5000.maf.gz 2014-04-21 14:13 680M
upstream2000.maf.gz 2014-04-21 13:25 327M
upstream1000.maf.gz 2014-04-21 12:51 197M
mm10.60way.commonNames.nh 2012-10-02 08:43 1.5K
mm10.60way.nh 2012-04-17 10:00 1.5K