This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz44way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the human genome (hg18, Mar. 2006):

    _ Human           Homo sapiens                   Mar. 2006   hg18
    _ Chimp           Pan troglodytes                Mar. 2006   panTro2
    _ Gorilla         Gorilla gorilla gorilla        Oct. 2008   gorGor1
    _ Orangutan       Pongo pygmaeus abelii          July 2007   ponAbe2
    _ Rhesus          Macaca mulatta                 Jan. 2006   rheMac2
    _ Marmoset        Callithrix jacchus             June 2007   calJac1
    _ Tarsier         Tarsius syrichta               Aug. 2008   tarSyr1
    _ Mouse lemur     Microcebus murinus             Jun. 2003   micMur1
    _ Bushbaby        Otolemur garnettii             Dec. 2006   otoGar1
    _ TreeShrew       Tupaia belangeri               Dec. 2006   tupBel1
    _ Mouse           Mus musculus                   July 2007   mm9
    _ Rat             Rattus norvegicus              Nov. 2004   rn4
    _ Kangaroo rat    Dipodomys ordii                July 2008   dipOrd1
    _ Guinea Pig      Cavia porcellus                Feb. 2008   cavPor3
    _ Squirrel        Spermophilus tridecemlineatus  Feb. 2008   speTri1
    _ Rabbit          Oryctolagus cuniculus          May  2005   oryCun1
    _ Pika            Ochotona princeps              July 2008   ochPri2
    _ Alpaca          Vicugna pacos                  July 2008   vicPac1
    _ Dolphin         Tursiops truncatus             Feb. 2008   turTru1
    _ Cow             Bos taurus                     Oct. 2007   bosTau4
    _ Horse           Equus caballus                 Sep. 2007   equCab2
    _ Cat             Felis catus                    Mar. 2006   felCat3
    _ Dog             Canis lupus familiaris         May  2005   canFam2
    _ Microbat        Myotis lucifugus               Mar. 2006   myoLuc1
    _ Megabat         Pteropus vampyrus              July 2008   pteVam1
    _ Hedgehog        Erinaceus europaeus            June 2006   eriEur1
    _ Shrew           Sorex araneus                  June 2006   sorAra1
    _ Elephant        Loxodonta africana             July 2008   loxAfr2
    _ Rock hyrax      Procavia capensis              July 2008   proCap1
    _ Tenrec          Echinops telfairi              July 2005   echTel1
    _ Armadillo       Dasypus novemcinctus           July 2008   dasNov2
    _ Sloth           Choloepus hoffmanni            July 2008   choHof1
    _ Opossum         Monodelphis domestica          Jan. 2006   monDom4
    _ Platypus        Ornithorhynchus anatinus       Mar. 2007   ornAna1
    _ Chicken         Gallus gallus                  May  2006   galGal3
    _ Zebra finch     Taeniopygia guttata            July 2008   taeGut1
    _ Lizard          Anolis carolinensis            Feb. 2007   anoCar1
    _ X. tropicalis   Xenopus tropicalis             Aug. 2005   xenTro2
    _ Tetraodon       Tetraodon nigroviridis         Feb. 2004   tetNig1
    _ Fugu            Takifugu rubripes              Oct. 2004   fr2
    _ Stickleback     Gasterosteus aculeatus         Feb. 2006   gasAcu1
    _ Medaka          Oryzias latipes                Oct. 2005   oryLat2
    _ Zebrafish       Danio rerio                    July 2007   danRer5
    _ Lamprey         Petromyzon marinus             Mar. 2007   petMar1


These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=cons44way
based on the phylogenetic tree: 44way.nh.

Files in this directory:
    - 44way.nh - phylogenetic tree for the phastCons and phyloP calculations
    - commonNames.nh - same as 44way.nh with the UCSC database name
	replace by the common name for the species

The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the human genome (hg18, Mar. 2006) aligned to the 
assemblies.

The maf/chr*.maf.gz files each contain all the alignments to that 
particular human chromosome, with additional annotations to
indicate gap context, genomic breaks, and quality scores for the
sequence in the underlying genome assemblies.

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

The SiepelLabCorrectedMafs directory contains a masked set of
32-way alignments.  Based on the 44-way, 2x MAFs, and the quality scores, 
the 32 species were extracted.

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/hg18/phastCons44way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way

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

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz44way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg18/multiz44way

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.
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[   ]44way.nh09-Jan-2009 11:41 1.2K 
[TXT]README.txt24-Feb-2011 12:56 6.4K 
[DIR]SiepelLabCorrectedMafs/27-Jan-2009 10:04 -  
[DIR]alignments/10-May-2011 16:54 -  
[   ]commonNames.nh13-Jan-2009 09:08 1.2K 
[DIR]maf/27-Jan-2009 13:09 -  

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