This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz100way/README.txt

This directory contains compressed multiple alignments of the following
assemblies to the human genome (hg19/GRCh37, Feb. 2009):

Assemblies used in these alignments:

== Primate subset ==
Human                    Homo sapiens                   Feb 2009  GRCh37/hg19                                   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                Nov 2008  Baylor Pham_1.0/papHam1                       Reciprocal best net 
Green monkey             Chlorocebus sabaeus            Jun 2013  Chlorocebus_sabeus 1.0/chlSab1                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              Mar 2012  RGSC 5.0/rn5                                  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                     Oct 2011  Baylor Btau_4.6.1/bosTau7                     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                    Sep 2011  ICGSC Felis_catus 6.2/felCat5                 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         Dec 2011  v3.0.1/chrPic1                                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                    Jul 2010  Zv9/danRer7                                   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=hg19&g=cons100way
based on the phylogenetic tree: hg19.100way.nh.

Files in this directory:
  - hg19.100way.nh - phylogenetic tree used during the multiz multiple alignment
  - hg19.100way.commonNames.nh - same as hg19.100way.nh with the UCSC database
       name replaced by the common name for the species
  - hg19.100way.scientificNames.nh - same as hg19.100way.nh with the UCSC
       database name replaced by the scientific name for the species

    See also:
http://genomewiki.ucsc.edu/index.php/Hg19_100way_conservation_alignment

The "alignments" directory contains compressed FASTA alignments
for the UCSC Known Gene CDS regions of the human genome (hg19/GRCh37, 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/hg19/phastCons100way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/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/hg19/multiz100way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg19/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.
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt21-Nov-2013 18:33 17K 
[DIR]alignments/12-Oct-2016 11:10 -  
[   ]hg19.100way.commonNames.nh11-Feb-2014 11:20 4.0K 
[   ]hg19.100way.nh11-Feb-2014 11:19 3.8K 
[   ]hg19.100way.scientificNames.nh11-Feb-2014 11:20 4.7K 
[DIR]maf/18-Oct-2013 16:32 -  
[TXT]md5sum.txt11-Feb-2014 21:36 337  
[   ]upstream1000.maf.gz11-Feb-2014 13:34 845M 
[   ]upstream2000.maf.gz11-Feb-2014 15:30 1.5G 
[   ]upstream5000.maf.gz11-Feb-2014 18:47 3.2G 

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