This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/multiz7way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the medium ground finch genome (geoFor1/GRCm38, Dec. 2011):

Assemblies used in these alignments:

==== reference assembly:
Medium ground finch - Geospiza fortis Apr. 2012  BGI/geoFor1       reference

==== Birds subset:
Zebra finch Taeniopygia guttata     Jul. 2008  WUGSC 3.2.4/taeGut1 Syntenic net
Budgerigar  Melopsittacus undulatus Sep. 2011  WUSTL v6.3/melUnd1  Syntenic net
Chicken  Gallus gallus              Nov. 2011  ICGSC 4.0/galGal4   Syntenic net
Turkey   Meleagris gallopavo        Dec. 2009  TGC 2.01/melGal1    Syntenic net

==== Vertebrate subset:
Human   Homo sapiens                Feb. 2009  GRCh37/hg19     Reciprocal best
Mouse   Mus musculus                Dec. 2019  GRCm38/mm10     Reciprocal best

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These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=geoFor1&g=cons7way
based on the phylogenetic tree: geoFor1.7way.nh.

Files in this directory:
 - geoFor1.7way.nh - phylogenetic tree used during the multiz multiple alignment
 - geoFor1.commonNames.7way.nh - same as geoFor1.7way.nh with the UCSC database
       name replaced by the common name for the species
 - upstream1000.xenoRefGene.maf.gz - alignments in regions upstream, see below
 - upstream2000.xenoRefGene.maf.gz - alignments in regions upstream, see below
 - upstream5000.xenoRefGene.maf.gz - alignments in regions upstream, see below

    See also:
http://genomewiki.ucsc.edu/index.php/GeoFor1_conservation_alignment

The "alignments" directory contains compressed FASTA alignments
for the Xeno RefSeq CDS regions of the medium ground finch genome
(geoFor1, Apr. 2012) aligned to the assemblies.

The maf/geoFor1.7way.maf.gz file contains the alignments to
the medium ground finch assembly, with additional annotations to
indicate gap context, and genomic breaks for the
sequence in the underlying genome assemblies.  Beware, the compressed
data size of these files is 1.5 Gb, uncompressed is approximately 7.5 Gb.

The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Xeno RefSeq 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 
mouse, 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 the medium ground finch; 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/geoFor1/phastCons7way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/phyloP7way

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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/geoFor1/multiz7way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/geoFor1/multiz7way

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.
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