This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/rn6/multiz20way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the Rat genome (rn6, Jul. 2014):

Assemblies used in these alignments:

Rat - Rattus norvegicus Jul. 2014 (RGSC 6.0/rn6) reference

Rat             Rattus norvegicus        Jul. 2014 (RGSC 6.0/rn6)

Mouse           Mus musculus             Dec. 2011 (GRCm38/mm10)
Prairie vole    Microtus ochrogaster     Oct 2012 (MicOch1.0/micOch1)
Guinea pig      Cavia porcellus          Feb. 2008 (Broad/cavPor3)
Rabbit          Oryctolagus cuniculus    Apr. 2009 (Broad/oryCun2)
Human           Homo sapiens             Dec. 2013 (GRCh38/hg38)
Chimp           Pan troglodytes          May 2016 (Pan_tro 3.0/panTro5)
Rhesus          Macaca mulatta           Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
Tarsier         Tarsius syrichta         Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)
Dog             Canis lupus familiaris   Sep. 2011 (Broad CanFam3.1/canFam3)
Panda           Ailuropoda melanoleuca   Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)
Cat             Felis catus              Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)
Cow             Bos taurus               Jun. 2014 (Bos_taurus_UMD_3.1.1/bosTau8)
Opossum         Monodelphis domestica    Oct. 2006 (Broad/monDom5)
Platypus        Ornithorhynchus anatinus Feb. 2007 (ASM227v2/ornAna2)
Chicken         Gallus gallus            Dec 2015 (Gallus_gallus-5.0/galGal5)
Turkey          Meleagris gallopavo      Nov. 2014 (Turkey_5.0/melGal5)
X. tropicalis   Xenopus tropicalis       Sep. 2012 (JGI 7.0/xenTro7)
Zebrafish       Danio rerio              Sep. 2014 (GRCz10/danRer10)
Elephant shark  Callorhinchus milii      Dec. 2013 (Callorhinchus_milii-6.1.3/calMil1)

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rn6&g=cons20way
based on the phylogenetic tree: rn6.20way.nh.

Files in this directory:
  - rn6.20way.nh - phylogenetic tree used during the multiz multiple alignment
  - rn6.20way.commonNames.nh - same as rn6.20way.nh with the UCSC database
	names replaced by the common name for the species
  - rn6.20way.scientificName.nh - same as rn6.20way.nh with the UCSC database
	names replaced by the scientific name for the species
  - upstream*.ensGene.maf.gz - alignments of regions upstream of Ensembl genes
  - rn6.20way.maf.gz - the multiple alignments on the Rat genome
  - md5sum.txt - md5 check sums of these files to verify correct download files

The "alignments" directory contains compressed FASTA alignments
for the CDS regions for the gene track ensGene (v86/Oct. 2016 version)
 of the rat genome (rn6, Jul. 2014) aligned to the assemblies.

The rn6.20way.maf.gz file contain all the alignments for the chromosomes
in the rat genome, including additional annotations to indicate gap
context and genomic breaks for the sequence in the underlying
genome assemblies.  Note, the compressed data size of the
maf file is 7.2 Gb, uncompressed is more than 46 Gb.

The .upstream*.*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for version v86/Oct. 2016 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 
the 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.

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/rn6/phastCons20way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/rn6/phyloP20way

---------------------------------------------------------------
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 7.9 Gb of compressed data in this directory.

Via rsync:
rsync -av --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/rn6/multiz20way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/rn6/multiz20way

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.
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[   ]upstream5000.ensGene.maf.gz24-Jan-2017 15:02 220M 
[   ]upstream2000.ensGene.maf.gz24-Jan-2017 14:57 103M 
[   ]upstream1000.ensGene.maf.gz24-Jan-2017 14:53 52M 
[   ]rn6.20way.scientificNames.nh24-Jan-2017 13:25 862  
[   ]rn6.20way.nh24-Jan-2017 13:25 683  
[   ]rn6.20way.maf.gz22-Jan-2017 10:39 7.2G 
[   ]rn6.20way.commonNames.nh24-Jan-2017 13:25 674  
[TXT]md5sum.txt24-Jan-2017 15:16 406  
[DIR]alignments/30-Jan-2017 11:01 -  
[TXT]README.txt30-Jan-2017 11:31 5.1K 

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