This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/micMur3/multiz3way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the Mouse lemur genome (micMur3, Feb. 2017):

Assemblies used in these alignments:                                (alignment
                                                                          type)


Mouse lemur - Microcebus murinus  Feb. 2017 (Broad/Mmur-3.0)       reference

Bushbaby    - Otolemur garnettii  Mar. 2011 (Broad/otoGar3)        syntenic
Human       - Homo sapiens        Dec. 2013 (GRCh38/hg38)          syntenic

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=micMur3&g=cons3way
based on the phylogenetic tree: micMur3.3way.nh.

Files in this directory:
  - micMur3.3way.nh - phylogenetic tree used during the multiz multiple alignment
  - micMur3.3way.commonNames.nh - same as micMur3.3way.nh with the UCSC database
	names replaced by the common name for the species
  - micMur3.3way.scientificName.nh - same as micMur3.3way.nh with the UCSC database
	names replaced by the scientific name for the species
  - micMur3.3way.maf.gz - the multiple alignments on the Mouse lemur genome
  - upstream*.ensGene.maf.gz: alignments to regions (1000, 2000 and 5000) bases 
    upstream of Ensembl genes. 
  - md5sum.txt - md5 check sums of these files to verify correct download files

The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the mouse lemur genome (micMur3, Feb. 2016)
aligned to the assemblies.

The micMur3.3way.maf.gz file contain all the alignments for the chromosomes
in the Mouse lemur 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 1.7 Gb, uncompressed is more than 6.2 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.cse.ucsc.edu/goldenPath/micMur3/phastCons3way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/micMur3/phyloP3way

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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 240 Mb of compressed data in this directory.

Via rsync:
rsync -av --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/micMur3/multiz3way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/micMur3/multiz3way

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.