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 - md5sum.txt 2005-05-24 10:03 607 chrM.maf.gz 2005-05-24 10:03 48K chr4h.maf.gz 2005-05-24 10:03 135K chrYh.maf.gz 2005-05-24 10:03 427K chrXh.maf.gz 2005-05-24 10:03 762K chr2h.maf.gz 2005-05-24 10:01 2.0M chr3h.maf.gz 2005-05-24 10:03 3.2M chr4.maf.gz 2005-05-24 10:03 3.3M chrU.maf.gz 2005-05-24 10:03 5.6M chr2R.maf.gz 2005-05-24 10:01 49M chrX.maf.gz 2005-05-24 10:03 53M chr2L.maf.gz 2005-05-24 10:01 55M chr3L.maf.gz 2005-05-24 10:02 58M chr3R.maf.gz 2005-05-24 10:03 68M