This directory contains compressed FASTA alignments for the CDS regions 
of the D. melanogaster genome (dm3, Apr. 2006, BDGP Release 5) aligned to
the following assemblies:

- 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:
  - flyBaseGene.exon*.fa.gz: for each exon in the dm3 FlyBase Gene track, this
    file contains either amino acids (AA) or nucleotides (Nuc) for dm3 and the
    aligning genomes.
  - refGene.exon*.fa.gz: for each exon in the dm3 RefSeq Gene track, this file 
    contains either amino acids (AA) or nucleotides (Nuc) for dm3 and the 
    aligning genomes.

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/alignments/

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.