This directory contains compressed multiple alignments of the 
following assemblies to the Medaka genome (oryLat2, Oct 2005):

  - stickleback (Feb 2006, gasAcu1) 
  - tetraodon (Feb 2004, tetNig1) 
  - fugu (Oct 2004, fr2) 
  - zebrafish (Jul 2007, danRer5) 

Files included in this directory:
  - oryLat2.5way.maf.gz - all alignments to the medaka genome
  - ensGene.upstream*.maf.gz: alignments to regions (1000, 2000 and 5000) bases 
    upstream of medaka Ensembl genes. 
  - oryLat2.5way.nh - phylogenetic tree used for the phastCons calculation

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/fr2/multiz5way. 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.