This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/multiz9way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the X. tropicalis genome (xenTro3, Nov 2009):

Assemblies used in these alignments:

 - X. tropicalis  Xenopus tropicalis         Nov. 2009  xenTro3/JGI 4.2
 - Lizard         Anolis carolinensis        May  2010  anoCar2/Broad
 - Chicken        Gallus gallus              May  2006  galGal3/WUGSC 2.1
 - Turkey         Meleagris gallopavo        Dec. 2009  melGal1/TGC Turkey_2.01
 - Opossum        Monodelphis domestica      Oct. 2006  monDom5/Broad
 - Rat            Rattus norvegicus          Nov. 2004  rn4/Baylor 3.4
 - Mouse          Mus musculus               Jul. 2007  mm9/NCBI37
 - Human          Homo sapiens               Feb. 2009  hg19/GRCh37   
 - Zebrafish      Danio rerio                Jul. 2010  danRer7/Zv9

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro3&g=cons9way
based on the phylogenetic tree: 9way.nh.

Files in this directory:
    - 9way.nh - phylogenetic tree used during the multiz multiple alignment
    - xenTro3.commonNames.9way.nh - same as 9way.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 (xenTro3, May 2010)
aligned to the assemblies.

The multiz9way.maf.gz file contains all the alignments for all contigs
in the X. tropicalis 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 3 Gb.  (664 Mb 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 
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/xenTro3/phastCons9way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/phyloP9way

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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 -av --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/multiz9way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/xenTro3/multiz9way

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.