This directory contains compressed multiple alignments of the 
following assemblies to the X. tropicalis genome (Aug 2005, xenTro2): 

  - chicken (Feb 2004, galGal2) 
  - opossum (Jan 2006, monDom4) 
  - human (Mar 2006, hg18) 
  - mouse (Feb 2006, mm8)
  - rat (Nov 2004, rn4)
  - zebrafish (Mar 2006, danRer4) 

Files included in this directory:
  - xenTro2.maf.gz: alignments to all xenTro2 scaffolds in MAF format
  - The maf/upstream*.maf.gz files contain alignments in regions upstream of
    annotated transcription starts for MGC 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 
    X. tropicalis, 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 X. tropicalis; 
    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.

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If you plan 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 to hgdownload.cse.ucsc.edu, 
then go to the directory goldenPath/xenTro2/multiz7way. To download 
multiple files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

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.