This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/dm6/multiz27way/README.txt This directory contains compressed multiple alignments of 23 drosophila sequences, house fly, anopheles mosquito, honey bee and red flour beetle. Files in this directory: dm6.27way.nh - Phylogenetic tree used for multiz alignment, UCSC database names dm6.27way.commonNames.nh - same phylogenetic tree, simple names dm6.27way.scientificNames.nh - same phylogenetic tree, scientific names maf/*.maf.gz - alignments referenced to dm6, separate maf files for each chromosome md5sum.txt - MD5 sums of these file to verify transmission For a description of multiple alignment format (MAF), see http://genome.ucsc.edu/goldenPath/help/maf.html. The phastCons data can be found at: http://hgdownload.cse.ucsc.edu/goldenPath/dm6/phastCons27way/ The phyloP data can be found at: http://hgdownload.cse.ucsc.edu/goldenPath/dm6/phyloP27way/ For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=dm6&g=cons27way Assemblies used in these alignments: (alignment type) D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) reference D. simulans Apr. 2005 (WUGSC 1.0/droSim1) syntenic D. sechellia Oct. 2005 (Broad/droSec1) syntenic D. yakuba Jun. 2006 (Flybase dyak_caf1/droYak3) syntenic D. erecta Feb. 2006 (Agencourt CAF1/droEre2) syntenic D. biarmipes Mar. 2013 (BCM Dbia_2.0/droBia2) syntenic D. suzukii Sep. 2013 (BGI Dsuzukii.v01/droSuz1) syntenic D. ananassae Feb. 2006 (Agencourt CAF1/droAna3) syntenic D. bipectinata Mar. 2013 (BCM Dbip_2.0/droBip2) syntenic D. eugracilis Mar. 2013 (modENCODE Deug_2.0/droEug2) syntenic D. elegans Mar. 2013 (BCM Dele_2.0/droEle2) syntenic D. kikkawai Mar. 2013 (BCM Dkik_2.0/droKik2) syntenic D. takahashii Mar. 2013 (BCM Dtak_2.0/droTak2) syntenic D. rhopaloa Feb. 2013 (modENCODE Drho_2.0/droRho2) syntenic D. ficusphila Mar. 2013 (BCM Dfic_2.0/droFic2) syntenic D. pseudoobscura Apr. 2013 (BCM Dpse_3.0/droPse3) syntenic D. persimilis Oct. 2005 (Broad/droPer1) syntenic D. miranda Apr. 2013 (U.C. Berkeley DroMir_2.2/droMir2) syntenic D. willistoni Aug. 2006 (JCVI dwil_caf1/droWil2) syntenic D. virilis Feb. 2006 (Agencourt CAF1/droVir3) syntenic D. mojavensis Feb. 2006 (Agencourt CAF1/droMoj3) syntenic D. albomicans May. 2012 (Kunming DroAlb_1.0/droAlb1) syntenic D. grimshawi Feb. 2006 (Agencourt CAF1/droGri2) syntenic Musca domestica Apr. 2013 (Glossina M_domestica-2.0.2/musDom2) net Anopheles gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) net Apis mellifera Nov. 2010 (BCM Amel_4.5/apiMel4) net Tribolium castaneum Sep. 2005 (BCM 2.0/triCas2) net --------------------------------------------------------------- To download a large file or multiple files from this directory, we recommend that you use rsync or ftp rather than downloading the files via our website. Via rsync: rsync -avz --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/dm6/multiz27way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/dm6/multiz27way To download multiple files from the UNIX command line, use the "mget" command. mget ... - 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. ---------------------------------------------------------------