This directory contains zipped multiple alignments of the following 
assemblies to the D. melanogaster genome (dm2, Apr. 2004):

- D. simulans (droSim1, Apr. 2005)
- D. yakuba (droYak1, Apr. 2004)
- D. ananassae (droAna1, Jul. 2004)
- D. pseudoobscura (dp3, Nov. 2004)
- D. virilis (droVir1, Jul. 2004) 
- D. mojavensis (droMoj1, Aug. 2004) 
- A. gambiae (anoGam1, Feb. 2003) 
- A. mellifera (apiMel1, Jul. 2004) 

The chr*.maf.gz files each contain all the alignments to that particular 
D. melanogaster chromosome.  

Pairwise alignments (chain and netted blastz alignments) can be found 
one directory level up in the vs*/axtNet/ directories (eg. dm2-droYak1 
alignments may be found in ../vsDroYak1/axtNet/chr*.axt.)  

For a description of the multiple alignment format (MAF), see

If you plan to download a large file or multiple files from this 
directory, we recommend you use ftp rather than downloading the files 
via our website. To do so, ftp to, then go to 
the directory goldenPath/dm2/multiz9way/. 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 available for public use. 
      Name                    Last modified      Size  Description
Parent Directory - chr2L.maf.gz 2005-05-24 10:01 55M chr2R.maf.gz 2005-05-24 10:01 49M chr2h.maf.gz 2005-05-24 10:01 2.0M chr3L.maf.gz 2005-05-24 10:02 58M chr3R.maf.gz 2005-05-24 10:03 68M chr3h.maf.gz 2005-05-24 10:03 3.2M chr4.maf.gz 2005-05-24 10:03 3.3M chr4h.maf.gz 2005-05-24 10:03 135K chrM.maf.gz 2005-05-24 10:03 48K chrU.maf.gz 2005-05-24 10:03 5.6M chrX.maf.gz 2005-05-24 10:03 53M chrXh.maf.gz 2005-05-24 10:03 762K chrYh.maf.gz 2005-05-24 10:03 427K md5sum.txt 2005-05-24 10:03 607