This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/monDom5/multiz9way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the opossum genome (monDom5, Oct. 2006):

    _ Opossum         Monodelphis domestica          Oct. 2006   monDom5
    _ Wallaby         Macropus eugenii               Nov. 2007   macEug1
    _ Human           Homo sapiens                   Mar. 2006   hg18
    _ Mouse           Mus musculus                   July 2007   mm9
    _ Dog             Canis lupus familiaris         May  2005   canFam2
    _ Platypus        Ornithorhynchus anatinus       Mar. 2007   ornAna1
    _ Chicken         Gallus gallus                  May  2006   galGal3
    _ X. tropicalis   Xenopus tropicalis             Aug. 2005   xenTro2
    _ Zebrafish       Danio rerio                    July 2007   danRer5

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=monDom5&g=multiz9way
based on the phylogenetic tree: 9way.nh.

Files in this directory:
    - 9way.nh - phylogenetic tree for the phastCons calculations

The maf/chr*.maf.gz files each contain all the alignments to that 
particular opossum chromosome, with additional annotations to
indicate gap context, genomic breaks, and quality scores for the
sequence in the underlying genome assemblies.

The maf/upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for 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 
opossum, 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 opossum; 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/hg18/phastCons9way

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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 5.8 Gb of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/monDom5/multi9way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/monDom5/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.