This directory contains compressed multiple alignments of the 
following assemblies to the Orangutan genome (ponAbe2, Jul. 2007):

    - orangutan       Pan troglodytes         July 2007, ponAbe2
    - human           Homo sapiens            Mar 2006, hg18
    - chimpanzee      Pan troglodytes         Mar 2006, panTro2
    - rhesus          Macaca mulatta          Jan 2006, rheMac2
    - marmoset        Callithrix jacchus      June 2007, calJac1
    - mouse           Mus musculus            July 2007, mm9
    - opossum         Monodelphis domestica   Jan 2006, monDom4
    - platypus        Ornithorhychus anatinus Mar 2007, ornAna1

These alignments were prepared using the methods described in the
track description file, multiz8way.html, based on the 
phylogenetic tree, 8way.nh.

The maf/chr*.maf.gz files each contain all the alignments to that 
particular Orangutan chromosome, with additional annotations to
indicate gap context and genomic breaks.

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 
orangutan, 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 orangutan; 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/ponAbe2/phastCons8way

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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/ponAbe2/multiz8way

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.