This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/felCat4/multiz6way/README.txt

This directory contains compressed multiple alignments of
of 5 mammal genomes to the cat genome (felCat4, Dec. 2008).

 Assemblies used in these alignments:


  - Cat             Felis catus             Dec 2008 felCat4  reference
  - Dog             Canis lupus familiaris  May 2005 canFam2  chain net
  - Panda           Ailuropoda melanoleuca  Dec 2009 ailMel1  recip best
  - Human           Homo sapiens            Feb 2009 hg19     chain net
  - Mouse           Mus musculus            Jul 2007 mm9      chain net
  - Opossum         Monodelphis domestica   Oct 2006 monDom5  chain net


These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=felCat4&g=cons6way
based on the phylogenetic tree: 6way.nh.

Files in this directory:
    - 6way.nh - phylogenetic tree used during the multiz multiple alignment
    - commonNames.6way.nh - same as 6way.nh with the UCSC database name
	replaced by the common name for the species

The felCat4.6way.maf.gz file contains all the alignments for all chromosomes
and contigs in the cat genome. Beware, the compressed
data size of this file is 2.2 GB.

The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for nscan 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/felCat4/phastCons6way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/felCat4/phyloP6way

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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/felCat4/multiz6way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/felCat4/multiz6way

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.