This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz4way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the human genome (hg38, Dec. 2013):

Assemblies used in these alignments:

Human              Homo sapiens             Dec. 2013 (GRCh38/hg38) reference

Mouse              Mus musculus             Dec. 2011 (GRCm38/mm10)
Chinese tree shrew Tupaia chinensis         Jan. 2013 (BGI TupChi_1.0/tupChi1)
Malayan flying lemur Galeopterus variegatus Jun. 2014 (WashU G_variegatus-3.0.2/galVar1)

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons4way
based on the phylogenetic tree: hg38.4way.nh.

Files in this directory:
  - hg38.4way.nh - phylogenetic tree used during the multiz multiple alignment
  - hg38.4way.commonNames.nh - same as hg38.4way.nh with the UCSC database
	names replaced by the common name for the species
  - hg38.4way.scientificName.nh - same as hg38.4way.nh with the UCSC database
	names replaced by the scientific name for the species
  - upstream*.knownGene.maf.gz - alignments of regions upstream of UCSC genes
  - hg38.4way.maf.gz - the multiple alignments on the human 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 knownGene (March 2016 version)
 of the human genome (hg38, Dec. 2013) aligned to the assemblies.

The hg38.4way.maf.gz file contain all the alignments for the chromosomes
in the human 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 3.0 Gb, uncompressed is more than 13 Gb.

The .upstream*.*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for version 81/July 2015  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 
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.

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/hg38/phastCons4way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP4way

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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/hg38/multiz4way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg38/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.

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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.