This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/rn5/multiz13way/README.txt

This directory contains compressed multiple alignments of the following
assemblies to the rat genome (rn5/RGSC 5.0, Mar. 2012):

Assemblies used in these alignments:

Rat                      Rattus norvegicus              Mar 2012  RGSC 5.0/rn5                                  Reference species
Chicken                  Gallus gallus                  Nov 2011  ICGSC Gallus_gallus-4.0/galGal4               Net
Chimp                    Pan troglodytes                Feb 2011  CSAC 2.1.4/panTro4                            Syntenic net
Cow                      Bos taurus                     Oct 2011  Baylor Btau_4.6.1/bosTau7                     Syntenic net
Dog                      Canis lupus familiaris         Sep 2011  Broad CanFam3.1/canFam3                       Syntenic net
Guinea pig               Cavia porcellus                Feb 2008  Broad/cavPor3                                 Syntenic net
Human                    Homo sapiens                   Dec 2013  GRCh38/hg38                                   Syntenic net
Mouse                    Mus musculus                   Dec 2011  GRCm38/mm10                                   Syntenic net
Opossum                  Monodelphis domestica          Oct 2006  Broad/monDom5                                 Net
Panda                    Ailuropoda melanoleuca         Dec 2009  BGI-Shenzhen 1.0/ailMel1                      Reciprocal best
Rhesus                   Macaca mulatta                 Oct 2010  BGI CR_1.0/rheMac3                            Syntenic net
Turkey                   Meleagris gallopavo            Dec 2009  TGC Turkey_2.01/melGal1                       Net
Zebrafish                Danio rerio                    Jul 2010  Zv9/danRer7                                   Net

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These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rn5&g=cons13way
based on the phylogenetic tree: rn5.13way.nh.

Files in this directory:
  - rn5.13way.nh - phylogenetic tree used during the multiz multiple alignment
  - rn5.13way.commonNames.nh - same as rn5.13way.nh with the UCSC database
       name replaced by the common name for the species
  - rn5.13way.scientificNames.nh - same as rn5.13way.nh with the UCSC
       database name replaced by the scientific name for the species

    See also:
http://genomewiki.ucsc.edu/index.php/rn5_13way_conservation_alignment
http://genomewiki.ucsc.edu/index.php/Rn5_13-way_Genome_size_statistics
http://genomewiki.ucsc.edu/index.php/Rn5_13-way_conservation_lastz_parameters

The "alignments" directory contains compressed FASTA alignments
for the Ensembl CDS regions of the rat genome (rn5/RGSC 5.0, Mar. 2012)
aligned to the assemblies.

The maf/chr*.maf.gz files each contain all the alignments to that particular
rat chromosome, with additional annotations to indicate gap context, and
genomic breaks for the sequence in the underlying genome assemblies.  Beware,
the compressed data size of these files is about 4.3 Gb, uncompressed
size is about 54 Gb.

The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Ensembl 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 
rat, 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 rat; 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/rn5/phastCons13way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/rn5/phyloP13way

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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/rn5/multiz13way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/rn5/multiz13way

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.

---------------------------------------------------------------
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.