This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the human genome (hg19/GRCh37, Feb. 2009):

Assemblies used in these alignments:

  - Human         Homo sapiens                  Feb. 2009  hg19/GRCh37
  - Chimp         Pan troglodytes               Mar. 2006  panTro2
  - Gorilla       Gorilla gorilla gorilla       Oct. 2008  gorGor1
  - Orangutan     Pongo pygmaeus abelii         July 2007  ponAbe2
  - Rhesus        Macaca mulatta                Jan. 2006  rheMac2
  - Baboon        Papio hamadryas               Nov. 2008  papHam1
  - Marmoset      Callithrix jacchus            June 2007  calJac1
  - Tarsier       Tarsius syrichta              Aug. 2008  tarSyr1
  - Mouse lemur   Microcebus murinus            Jul. 2007  micMur1
  - Bushbaby      Otolemur garnettii            Dec. 2006  otoGar1
  - Tree shrew    Tupaia belangeri              Dec. 2006  tupBel1
  - Mouse         Mus musculus                  July 2007  mm9   
  - Rat           Rattus norvegicus             Nov. 2004  rn4   
  - Kangaroo rat  Dipodomys ordii               Jul. 2008  dipOrd1
  - Guinea Pig    Cavia porcellus               Feb. 2008  cavPor3
  - Squirrel      Spermophilus tridecemlineatus Feb. 2008  speTri1
  - Rabbit        Oryctolagus cuniculus         Apr. 2009  oryCun2
  - Pika          Ochotona princeps             Jul. 2008  ochPri2
  - Alpaca        Vicugna pacos                 Jul. 2008  vicPac1
  - Dolphin       Tursiops truncatus            Feb. 2008  turTru1
  - Cow           Bos taurus                    Oct. 2007  bosTau4
  - Horse         Equus caballus                Sep. 2007  equCab2
  - Cat           Felis catus                   Mar. 2006  felCat3
  - Dog           Canis lupus familiaris        May  2005  canFam2
  - Microbat      Myotis lucifugus              Mar. 2006  myoLuc1
  - Megabat       Pteropus vampyrus             Jul. 2008  pteVam1
  - Hedgehog      Erinaceus europaeus           June 2006  eriEur1
  - Shrew         Sorex araneus                 June 2006  sorAra1
  - Elephant      Loxodonta africana            Jul. 2009  loxAfr3
  - Rock hyrax    Procavia capensis             Jul. 2008  proCap1
  - Tenrec        Echinops telfairi             July 2005  echTel1
  - Armadillo     Dasypus novemcinctus          Jul. 2008  dasNov2
  - Sloth         Choloepus hoffmanni           Jul. 2008  choHof1
  - Wallaby       Macropus eugenii              Nov. 2007  macEug1
  - Opossum       Monodelphis domestica         Oct. 2006  monDom5
  - Platypus      Ornithorhynchus anatinus      Mar. 2007  ornAna1
  - Chicken       Gallus gallus                 May  2006  galGal3
  - Zebra finch   Taeniopygia guttata           Jul. 2008  taeGut1
  - Lizard        Anolis carolinensis           Feb. 2007  anoCar1
  - X. tropicalis Xenopus tropicalis            Aug. 2005  xenTro2
  - Tetraodon     Tetraodon nigroviridis        Mar. 2007  tetNig2
  - Fugu          Takifugu rubripes             Oct. 2004  fr2   
  - Stickleback   Gasterosteus aculeatus        Feb. 2006  gasAcu1
  - Medaka        Oryzias latipes               Oct. 2005  oryLat2
  - Zebrafish     Danio rerio                   Dec. 2008  danRer6
  - Lamprey       Petromyzon marinus            Mar. 2007  petMar1

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way
based on the phylogenetic tree: 46way.nh.

Files in this directory:
    - 46way.nh - phylogenetic tree used during the multiz multiple alignment
    - commonNames.46way.nh - same as 46way.nh with the UCSC database name
	replaced by the common name for the species

UPDATE - January 2010 - corrected tree diagram
    - 46way.corrected.nh - Wallaby has moved to be a sister to Opossum in
	the tree diagram from the above 46way.nh
    - commonNames.46way.corrected.nh - Wallaby has moved to be a sister to
	Opossum in the tree diagram from the above commonNames.46way.nh
    See also:
http://genomewiki.ucsc.edu/index.php/Human/hg19/GRCh37_46-way_multiple_alignment

The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the human genome (hg19/GRCh37, Feb. 2009)
aligned to the assemblies.

The maf/chr*.maf.gz files each contain all the alignments to that 
particular human chromosome, with additional annotations to
indicate gap context, genomic breaks, and quality scores for the
sequence in the underlying genome assemblies.  Beware, the compressed
data size of these files is 31 Gb, uncompressed is more than 250 Gb.

The maf/upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for RefSeq genes with annotated 5' UTRs.
These files differ from the standard MAF format: they display
alignments that extend from start to end of the upstream region in 
human, whether or not alignments actually exist. In situations where no  
alignments exist or the alignments of one or more species are missing, 
dot (".") is used as a placeholder. Multiple regions of an assembly's
sequence may align to a single region in human; therefore, only the 
species name is displayed in the alignment data and no position information 
is recorded. The alignment score is always zero in these files. These files
are updated weekly.

For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.

PhastCons conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP46way

---------------------------------------------------------------
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.
There is approximately 31 Gb of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg19/multiz46way

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  -  
[DIR]alignments/21-Apr-2014 17:09 -  
[DIR]maf/01-Dec-2009 08:06 -  
[DIR]mafLinks/15-Dec-2014 17:10 -  
[TXT]md5sum.txt05-Jan-2010 15:20 216  
[   ]46way.corrected.nh05-Jan-2010 15:12 1.2K 
[   ]46way.nh27-Aug-2009 11:19 1.2K 
[   ]commonNames.46way.corrected.nh05-Jan-2010 15:19 1.2K 
[   ]commonNames.46way.nh03-Nov-2009 14:22 1.2K 
[TXT]README.txt08-Oct-2012 09:22 6.7K 

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