This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/danRer6/multiz6way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the zebrafish genome (danRer6, Dec. 2008):

Assemblies used in these alignments:

  - Zebrafish     Danio rerio                   Dec. 2008  danRer6
  - Tetraodon     Tetraodon nigroviridis        Mar. 2007  tetNig2
  - Stickleback   Gasterosteus aculeatus        Feb. 2006  gasAcu1
  - X. tropicalis Xenopus tropicalis            Aug. 2005  xenTro2
  - Mouse         Mus musculus                  July 2007  mm9   
  - Human         Homo sapiens                  Feb. 2009  hg19/GRCh37

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer6&g=multiz6way
based on the phylogenetic tree: 6way.nh.

Files in this directory:
    - 6way.nh - phylogenetic tree used during the multiz multiple alignment

The maf/multiz6way.maf.gz file contains all the alignments to the
chromosomes and scaffolds, 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 734 MB, uncompressed is much more.

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/danRer6/phastCons6way

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

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer6/multiz6way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/danRer6/multiz6way

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.

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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.