This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/multiz11way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the Gorilla genome (gorGor3, May 2011):

Assemblies used in these alignments:

Gorilla gorilla gorilla                 May  2011   Sanger gorGor3.1/gorGor3
Chimp           Pan troglodytes         Oct. 2010   CGSC 2.1.3/panTro3
Human           Homo sapiens            Feb. 2009   GRCh37/hg19
Gibbon          Nomascus leucogenys     Jan. 2010   GGSC Nleu1.0/nomLeu1
Orangutan       Pongo pygmaeus abelii   Jul. 2007   WUGSC 2.0.2/ponAbe2
Baboon          Papio hamadryas         Nov. 2008   Baylor 1.0/papHam1
Rhesus          Macaca mulatta          Jan. 2006   MGSC Merged 1.0/rheMac2
Marmoset        Callithrix jacchus      Mar. 2009   WUGSC 3.2/calJac3
Tarsier         Tarsius syrichta        Aug. 2008   Broad/tarSyr1
Mouse lemur     Microcebus murinus      Jun. 2003   Broad/micMur1
Bushbaby        Otolemur garnettii      Dec. 2006   Broad/otoGar1

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=gorGor3&g=cons11way
based on the phylogenetic tree: gorGor3.11way.nh.

Files in this directory:
    - gorGor3.11way.nh - phylogenetic tree used during the
			multiz multiple alignment
    - gorGor3.commonNames.11way.nh - same as 11way.nh with the UCSC database
	names replaced by the common name for the species

The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the zebrafish genome (gorGor3, May 2010)
aligned to the assemblies.

The multiz11way.maf.gz file contains all the alignments for all contigs
in the X. tropicalis genome.  Additional annotations to indicate gap
context and genomic breaks for the sequence in the underlying genome
assemblies.  Beware, the uncompressed
data size of this file is 28 Gb.  (3.8 Gb compressed)

The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for 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. 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/gorGor3/phastCons11way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/phyloP11way

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

Via rsync:
rsync -av --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/multiz11way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/gorGor3/multiz11way

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.