This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/danRer10/multiz12way/README.txt

This directory contains compressed multiple alignments of
12 genomes to the Danio rerio/danRer10/Sept. 2014 zebrafish genome.

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer10&g=cons12way
based on the phylogenetic tree: danRer10.12way.nh.

danRer10.12way.maf.gz
Files in this directory:
  - danRer10.12way.nh - phylogenetic tree used during the multiz multiple
        alignment, using the UCSC database name, or sequence name for those
        sequences that are not hosted in UCSC databases.
  - danRer10.12way.scientificName.nh - same as danRer10.12way.nh with the
        sequence name replaced with the scientific name for the species.
  - danRer10.12way.commonNames.nh - same as danRer10.12way.nh with the sequence
        name replaced with the common name
  - danRer10.12way.maf.gz - multiple alignments on zebrafish
  - upstream*.ensGene.maf.gz - alignments of regions upstream of
      Ensembl genes
  - md5sum.txt - md5 check sums of these files to verify correct download files

The "alignments" directory contains compressed FASTA alignments
for the CDS regions for the gene track: ensGene,
 of the zebrafish genome (danRer10, Sept. 2014) aligned to the assemblies.

The danRer10.12way.maf.gz file contains all the alignments on the zebrafish
genome, including additional annotations to indicate gap
context and genomic breaks for the sequence in the underlying
genome assemblies.  Note, the compressed data size of these
maf files is 1.2 Gb, uncompressed is approximately 5.4 Gb.

The upstream*.ensGene.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Ensembl 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 
chicken, 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 chicken; 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.

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/danRer10/phastCons12way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/danRer10/phyloP12way

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Assemblies used in these alignments:

Zebrafish       Danio rerio     Sep. 2014 (GRCz10/danRer10) (reference)

Stickleback     Gasterosteus aculeatus  Feb. 2006 (Broad/gasAcu1) (maf net)
Medaka  Oryzias latipes Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (maf net)
Tetraodon       Tetraodon nigroviridis  Mar. 2007
                (Genoscope 8.0/tetNig2) (maf net)
Fugu    Takifugu rubripes       Oct. 2011 (FUGU5/fr3) (maf net)
Spotted gar     Lepisosteus oculatus    Dec 2011 (LepOcu1/lepOcu1) (maf net)
Human   Homo sapiens    Dec. 2013 (GRCh38/hg38) (maf net)
Mouse   Mus musculus    Dec. 2011 (GRCm38/mm10) (maf net)
Chicken Gallus gallus   Mar. 2018 (GRCg6a/galGal6) (maf net)
X. tropicalis   Xenopus tropicalis      Jul. 2016
                (Xenopus_tropicalis_v9.1/xenTro9) (maf net)
Coelacanth      Latimeria chalumnae     Aug. 2011 (Broad/latCha1) (maf net)
Elephant shark  Callorhinchus milii     Dec. 2013
                (Callorhinchus_milii-6.1.3/calMil1) (maf 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.
There is approximately 40 Gb of compressed data in this directory,
approximately 340 Gb uncompressed.

Via rsync:
rsync -av --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer10/multiz12way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/danRer10/multiz12way

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.