This directory contains compressed FASTA alignments for the CDS regions
of the human genome (hg19/GRCh37, Feb. 2009) aligned to the 
following assemblies:

  - Human         Homo sapiens                  Feb. 2009  hg19/GRCh37
  - Chimp         Pan troglodytes               Mar. 2006  panTro2
  - Gorilla       Gorilla gorilla gorilla       Oct. 2008  gorGor1
  - Orangutan     Pongo pygmaeus abelii         July 2007  ponAbe2
  - Rhesus        Macaca mulatta                Jan. 2006  rheMac2
  - Baboon        Papio hamadryas               Nov. 2008  papHam1
  - Marmoset      Callithrix jacchus            June 2007  calJac1
  - Tarsier       Tarsius syrichta              Aug. 2008  tarSyr1
  - Mouse lemur   Microcebus murinus            Jun. 2003  micMur1
  - Bushbaby      Otolemur garnettii            Dec. 2006  otoGar1
  - Tree shrew    Tupaia belangeri              Dec. 2006  tupBel1
  - Mouse         Mus musculus                  July 2007  mm9   
  - Rat           Rattus norvegicus             Nov. 2004  rn4   
  - Kangaroo rat  Dipodomys ordii               Jul. 2008  dipOrd1
  - Guinea Pig    Cavia porcellus               Feb. 2008  cavPor3
  - Squirrel      Spermophilus tridecemlineatus Feb. 2008  speTri1
  - Rabbit        Oryctolagus cuniculus         Apr. 2009  oryCun2
  - Pika          Ochotona princeps             Jul. 2008  ochPri2
  - Alpaca        Vicugna pacos                 Jul. 2008  vicPac1
  - Dolphin       Tursiops truncatus            Feb. 2008  turTru1
  - Cow           Bos taurus                    Oct. 2007  bosTau4
  - Horse         Equus caballus                Sep. 2007  equCab2
  - Cat           Felis catus                   Mar. 2006  felCat3
  - Dog           Canis lupus familiaris        May  2005  canFam2
  - Microbat      Myotis lucifugus              Mar. 2006  myoLuc1
  - Megabat       Pteropus vampyrus             Jul. 2008  pteVam1
  - Hedgehog      Erinaceus europaeus           June 2006  eriEur1
  - Shrew         Sorex araneus                 June 2006  sorAra1
  - Elephant      Loxodonta africana            Jul. 2009  loxAfr3
  - Rock hyrax    Procavia capensis             Jul. 2008  proCap1
  - Tenrec        Echinops telfairi             July 2005  echTel1
  - Armadillo     Dasypus novemcinctus          Jul. 2008  dasNov2
  - Sloth         Choloepus hoffmanni           Jul. 2008  choHof1
  - Wallaby       Macropus eugenii              Nov. 2007  macEug1
  - Opossum       Monodelphis domestica         Oct. 2006  monDom5
  - Platypus      Ornithorhynchus anatinus      Mar. 2007  ornAna1
  - Chicken       Gallus gallus                 May  2006  galGal3
  - Zebra finch   Taeniopygia guttata           Jul. 2008  taeGut1
  - Lizard        Anolis carolinensis           Feb. 2007  anoCar1
  - X. tropicalis Xenopus tropicalis            Aug. 2005  xenTro2
  - Tetraodon     Tetraodon nigroviridis        Mar. 2007  tetNig2
  - Fugu          Takifugu rubripes             Oct. 2004  fr2   
  - Stickleback   Gasterosteus aculeatus        Feb. 2006  gasAcu1
  - Medaka        Oryzias latipes               Oct. 2005  oryLat2
  - Zebrafish     Danio rerio                   Dec. 2008  danRer6
  - Lamprey       Petromyzon marinus            Mar. 2007  petMar1

Files included in this directory:
  - knownGene.exon*.fa.gz: for each exon in the hg19/GRCh37 UCSC Gene track,
    this file contains either amino acids (AA) or nucleotides (Nuc) for
    hg19/GRCh37 and the aligning genomes.
  - knownCanonical.exon*.fa.gz: for each exon in the hg19/GRCh37 canonical
    set of UCSC Genes, this file contains either amino acids (AA) or
    nucleotides (Nuc) for hg19/GRCh37 and the aligning genomes.
  - refGene.exon*.fa.gz: for each exon in the hg19/GRCh37 RefSeq Gene track,
    this file contains either amino acids (AA) or nucleotides (Nuc) for
    hg19/GRCh37 and the aligning genomes.

For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html
and http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FASTA.

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To download a large file or multiple files from this directory, we recommend 
that you use ftp rather than downloading the files via our website. To do so: 
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg19/multiz46way/alignments

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.

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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.