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 http://genome.ucsc.edu/goldenPath/help/maf.html. --------------------------------------------------------- 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 hgdownload.cse.ucsc.edu, then go to the directory goldenPath/dm2/multiz9way/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) All the files in this directory are freely available for public use.