This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/multiz7way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the lizard genome (anoCar2, May 2010):

Assemblies used in these alignments:

  - Lizard         Anolis carolinensis        May  2010  anoCar2/Broad
  - Chicken        Gallus gallus              May  2006  galGal3/WUGSC 2.1
  - Platypus       Ornithorhynchus anatinus   Mar. 2007  ornAna1/WUGSC 5.0.1
  - Human          Homo sapiens               Feb. 2009  hg19/GRCh37   
  - Mouse          Mus musculus               July 2007  mm9/NCBI37
  - X. tropicalis  Xenopus tropicalis         Aug. 2005  xenTro2/JGI 4.1
  - Stickleback    Gasterosteus aculeatus     Feb. 2006  gasAcu1/Broad

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=anoCar2&g=cons7way
based on the phylogenetic tree: 7way.nh.

Files in this directory:
    - 7way.nh - phylogenetic tree used during the multiz multiple alignment
    - anoCar2.commonNames.7way.nh - same as 7way.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 (anoCar2, May 2010)
aligned to the assemblies.

The multiz7way.maf.gz file contains all the alignments for all chromosomes
and contigs in the lizard 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.  (780 Mb compressed)

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/anoCar2/phastCons7way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/phyloP7way

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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/anoCar2/multiz7way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/anoCar2/multiz7way

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.