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
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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.
---------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
alignments/ 2014-12-12 08:35 -
dm6.27way.commonNames.nh 2014-11-14 09:06 1.0K
dm6.27way.nh 2014-11-14 09:06 1.0K
dm6.27way.scientificNames.nh 2014-11-14 09:06 1.3K
maf/ 2019-11-06 10:50 -
md5sum.txt 2014-11-20 09:47 169