This directory contains compressed multiple alignments of the 
following assemblies to the Marmoset genome (calJac1, June 2007):

  - marmoset        Callithrix jacchus      June 2007, calJac1  reference
  - rhesus          Macaca mulatta          Jan 2006, rheMac2   recip best net
  - orangutan       Pongo pygmaeus abelii   July 2007, ponAbe2  recip best net
  - chimpanzee      Pan troglodytes         Mar 2006, panTro2   recip best net
  - human           Homo sapiens            Mar 2006, hg18      recip best net
  - mouse           Mus musculus            July 2007, mm9      recip best net
  - dog             Canis familiaris        May 2005, canFam2   recip best net
  - opossum         Monodelphis domestica   Jan 2006, monDom4   chain net
  - platypus        Ornithorhychus anatinus Mar 2007, ornAna1   chain net

These alignments were prepared using the methods described in the
track description file, multiz9way.html, based on the 
phylogenetic tree, 9way.nh.

The calJac1.9way.maf.gz file contains all the alignments to the 
Marmoset contigs, with additional annotations to indicate gap context.

The maf/upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Xeno 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 
marmoset, 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 marmoset; 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/calJac1/phastCons9way

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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/calJac1/multiz9way

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.