This file is from:

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:
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:

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

PhastCons conservation scores for these alignments are available at:

PhyloP conservation scores for these alignments are available at:

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:// ./

Via FTP:
    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
      Name                      Last modified      Size  Description
Parent Directory - alignments/ 2019-10-11 12:04 - maf/ 2019-11-06 11:04 - md5sum.txt 2014-04-22 10:28 270 mm10.60way.commonNames.nh 2012-10-02 08:43 1.5K mm10.60way.nh 2012-04-17 10:00 1.5K upstream1000.maf.gz 2014-04-21 12:51 197M upstream2000.maf.gz 2014-04-21 13:25 327M upstream5000.maf.gz 2014-04-21 14:13 680M