This file is from:

    http://hgdownload-test.cse.ucsc.edu/goldenPath/mm10/multiz4way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the mouse genome (mm10, Dec. 2011):

Assemblies used in these alignments:

Mouse              Mus musculus             Dec. 2011 (GRCm38/mm10) (reference)

Malayan flying lemur Galeopterus variegatus Jun. 2014 (WashU/galVar1)
Human              Homo sapiens             Dec. 2013 (GRCh38/hg38)
Chinese tree shrew Tupaia chinensis         Jan. 2013 (BGI/tupChi1)

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=cons4way
based on the phylogenetic tree: mm10.4way.nh.

Files in this directory:
 - mm10.4way.nh - phylogenetic tree used during the multiz multiple alignment
 - mm10.4way.commonNames.nh - same as mm10.4way.nh with the UCSC database
	names replaced by the common name for the species
 - mm10.4way.scientificName.nh - same as mm10.4way.nh with the UCSC
	database names replaced by the scientific name for the species
 - mm10.4way.maf.gz - the multiple alignments on the mouse genome
 - md5sum.txt - md5 check sums of these files to verify correct download files

The mm10.4way.maf.gz file contain all the alignments for the chromosomes
in the mouse 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 2.0 Gb, uncompressed is 7.1 Gb.

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-test.cse.ucsc.edu/goldenPath/mm10/phastCons4way

PhyloP conservation scores for these alignments are available at:
http://hgdownload-test.cse.ucsc.edu/goldenPath/mm10/phyloP4way

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

Via rsync:
rsync -av --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/multiz4way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/mm10/multiz4way

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.

      Name                          Last modified      Size  Description
      Parent Directory                                   -   
      md5sum.txt                    2017-04-21 21:04  412   
      upstream5000.knownGene.maf.gz 2017-04-21 20:49   97M  
      upstream2000.knownGene.maf.gz 2017-04-21 20:45   45M  
      upstream1000.knownGene.maf.gz 2017-04-21 20:42   25M  
      mm10.4way.scientificNames.nh  2017-04-21 20:37  132   
      mm10.4way.commonNames.nh      2017-04-21 20:37  118   
      mm10.4way.nh                  2017-04-21 20:37   90   
      alignments/                   2017-04-21 18:52    -   
      mm10.4way.maf.gz              2017-04-20 22:27  1.9G