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: <your email address>
    go to the directory goldenPath/dm6/multiz27way

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.
---------------------------------------------------------------
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt21-Nov-2014 12:42 4.4K 
[DIR]alignments/20-Nov-2014 10:34 -  
[   ]dm6.27way.commonNames.nh14-Nov-2014 09:06 1.0K 
[   ]dm6.27way.nh14-Nov-2014 09:06 1.0K 
[   ]dm6.27way.scientificNames.nh14-Nov-2014 09:06 1.3K 
[DIR]maf/14-Nov-2014 09:05 -  
[TXT]md5sum.txt20-Nov-2014 09:47 169  

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