This directory contains compressed FASTA alignments for the CDS regions
of the mouse genome (mm9, Mar. 2006) aligned to the 
following assemblies:

    _ mouse           Mus musculus            July 2007, mm9
    _ rat             Rattus norvegicus       Nov 2004, rn4
    _ guinea pig      Cavia porcellus         Oct 2005, cavPor2
    _ rabbit          Oryctolagus cuniculus   May 2005, oryCun1
    _ human           Homo sapiens            Mar 2006, hg18
    _ chimpanzee      Pan troglodytes         Mar 2006, panTro2
    _ orangutan       Pongo pygmaeus abelii   July 2007, ponAbe2
    _ rhesus          Macaca mulatta          Jan 2006, rheMac2
    _ marmoset        Callithrix jacchus      June 2007, calJac1
    _ bushbaby        Otolemur garnetti       Dec 2006, otoGar1
    _ tree shrew      Tupaia belangeri        Dec 2006, tupBel1
    _ shrew           Sorex araneus           June 2006, sorAra1
    _ hedgehog        Erinaceus europaeus     June 2006, eriEur1
    _ dog             Canis familiaris        May 2005, canFam2
    _ cat             Felis catus             Mar 2006, felCat3
    _ horse           Equus caballus          Jan 2007, equCab1
    _ cow             Bos taurus              Aug 2006, bosTau3
    _ armadillo       Dasypus novemcinctus    May 2005, dasNov1
    _ elephant        Loxodonta africana      May 2005, loxAfr1
    _ tenrec          Echinops telfairi       July 2005, echTel1
    _ opossum         Monodelphis domestica   Jan 2006, monDom4
    _ platypus        Ornithorhychus anatinus Mar 2007, ornAna1
    _ chicken         Gallus gallus           May 2006, galGal3
    _ lizard          Anolis carolinensis     Feb 2007, anoCar1
    _ frog            Xenopus tropicalis      Aug 2005, xenTro2
    _ tetraodon       Tetraodon nigroviridis  Feb 2004, tetNig1
    _ fugu            Takifugu rubripes       Oct 2004, fr2
    _ stickleback     Gasterosteus aculeatus  Feb 2006, gasAcu1
    _ medaka          Oryzias latipes         Apr 2006, oryLat1
    _ zebrafish       Danio rerio             July 2007, danRer5

Files included in this directory:
  - knownGene.exon*.fa.gz: for each exon in the mm9 UCSC Gene track, this
    file contains either amino acids (AA) or nucleotides (Nuc) for mm9 and
    the aligning genomes.
  - knownCanonical.exon*.fa.gz: for each exon in the mm9 canonical set of
    UCSC Genes, this file contains either amino acids (AA) or 
    nucleotides (Nuc) for mm9 and the aligning genomes.
  - refGene.exon*.fa.gz: for each exon in the mm9 RefSeq Gene track, this
    file contains either amino acids (AA) or nucleotides (Nuc) for mm9 
    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/mm9/multiz30way/alignment

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.