This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/panTro3/multiz12way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the chimp genome (panTro3, Oct. 2010):

Assemblies used in these alignments:

  - Chimp         Pan troglodytes               Oct. 2010  panTro3
  - Human         Homo sapiens                  Feb. 2009  hg19/GRCh37
  - Orangutan     Pongo pygmaeus abelii         July 2007  ponAbe2   
  - Rhesus        Macaca mulatta                Jan. 2006  rheMac2   
  - Marmoset      Callithrix jacchus            Mar. 2009  calJac3   
  - Mouse         Mus musculus                  July 2007  mm9   
  - Rat           Rattus norvegicus             Nov. 2004  rn4
  - Horse         Equus caballus                Sep. 2007  equCab2
  - Dog           Canis lupus familiaris        May. 2005  canFam2     
  - Opossum       Monodelphis domestica         Oct. 2006  monDom5
  - Chicken       Gallus gallus                 May. 2006  galGal3
  - Zebrafish     Danio rerio                   Jul. 2010  danRer7

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=panTro3&g=cons12way
based on the phylogenetic tree: 12way.nh.

Files in this directory:
    - 12way.nh - phylogenetic tree used during the multiz multiple alignment
    - panTro3.commonNames.12way.nh - same as 12way.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 chimp genome (panTro3, Oct. 2010)
aligned to the assemblies.

The multiz12way.maf.gz file contains all the alignments for all chromosomes
and contigs in the chimp genome.
Additional annotations to indicate gap context and genomic breaks for the
sequence in the underlying genome assemblies.  Beware, the compressed
data size of this file is 11 Gb, uncompressed is more than 56 Gb.

The maf/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 chimp; 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/panTro3/phastCons12way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/panTro3/phyloP12way

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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/panTro3/multiz12way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/panTro3/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.

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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.