This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/fr3/multiz8way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the Fugu genome (fr3, Oct. 2011):

Assemblies used in these alignments:

Fugu            Takifugu rubripes       Oct. 2011   FUGU5/fr3
Tetraodon       Tetraodon nigroviridis  Mar. 2007   Genoscope 8.0/tetNig2
Nile tilapia    Oreochromis niloticus   Jan. 2011   Broad/oreNil1
Stickleback     Gasterosteus aculeatus  Feb. 2006   Broad/gasAcu1
Atlantic cod    Gadus morhua            May. 2010   Genofisk/gadMor1
Medaka          Oryzias latipes         Oct. 2005   NIG/oryLat2
Zebrafish       Danio rerio             Jul. 2010   Zv9/danRer7
Coelacanth      Latimeria chalumnae     Aug. 2011   Broad/latCha1

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=fr3&g=cons8way
based on the phylogenetic tree: fr3.8way.nh.

Files in this directory:
    - fr3.8way.nh - phylogenetic tree used during the
			multiz multiple alignment
    - fr3.commonNames.8way.nh - same as 8way.nh with the UCSC database
	names replaced by the common name for the species

The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the zebrafish genome (fr3, Oct. 2011)
aligned to the assemblies.

The multiz8way.maf.gz file contains all the alignments for all contigs
in the Fugu genome.  Additional annotations to indicate gap
context and genomic breaks for the sequence in the underlying genome
assemblies.  Beware, the uncompressed
data size of this file is 28 Gb.  (3.8 Gb compressed)

The upstream*.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 
fugu, 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 fugu; 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/fr3/phastCons8way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/fr3/phyloP8way

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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 3.0 Gb of compressed data in this directory.

Via rsync:
rsync -av --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/multiz8way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/fr3/multiz8way

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.