This directory contains compressed multiple alignments of the 
following assemblies to the D. melanogaster genome
(dm3, Apr. 2006, BDGP Release 5)

- D. simulans (droSim1, Apr. 2005)
- D. sechellia (droSec1, Oct. 2005)
- D. yakuba (droYak2, Nov. 2005)
- D. erecta (droEre2, Feb. 2006)
- D. ananassae (droAna3, Feb. 2006)
- D. pseudoobscura (dp4, Feb. 2006) 
- D. persimilis (droPer1, Oct. 2005)
- D. willistoni (droWil1, Feb. 2006)
- D. virilis (droVir3, Feb. 2006) 
- D. mojavensis (droMoj3, Feb. 2006) 
- D. grimshawi (droGri2, Feb. 2006)
- A. gambiae (anoGam1, Feb. 2003) 
- A. mellifera (apiMel3, May 2005) 
- T. castaneum (triCas2, Sep. 2005)

Files included in this directory:
  - chr*.maf.gz files: each contain all the alignments to that 
    particular D. melanogaster chromosome.  
  - The maf/upstream*.maf.gz files contain alignments in regions 
    upstream of annotated transcription starts for FlyBase 5.12 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 D. melanogaster, 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 D. melanogaster; 
    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.

For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.

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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/dm3/multiz15way

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.

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.