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

    _ human           Homo sapiens            Mar 2006, hg18
    _ chimpanzee      Pan troglodytes         Mar 2006, panTro2
    _ rhesus          Macaca mulatta          Jan 2006, rheMac2
    _ bushbaby        Otolemur garnetti       Dec 2006, otoGar1
    _ tree shrew      Tupaia belangeri        Dec 2006, tupBel1
    _ mouse           Mus musculus            Feb 2006, mm8
    _ rat             Rattus norvegicus       Nov 2004, rn4
    _ guinea pig      Cavia porcellus         Oct 2005, cavPor2
    _ rabbit          Oryctolagus cuniculus   May 2005, oryCun1
    _ shrew           Sorex araneus           June 2006, sorAra1
    _ hedgehog        Erinaceus europaeus     June 2006, eriEur1
    _ dog             Canis familiaris        May 2005, canFam2
    _ cat             Felis catus             Mar 2006, felCat3
    _ horse           Equus caballus          Feb 2007, equCab1
    _ cow             Bos taurus              Aug 2006, bosTau3
    _ armadillo       Dasypus novemcinctus    May 2005, dasNov1
    _ elephant        Loxodonta africana      May 2005, loxAfr1
    _ tenrec          Echinops telfairi       July 2005, echTel1
    _ opossum         Monodelphis domestica   Jan 2006, monDom4
    _ platypus        Ornithorhychus anatinus Mar 2007, ornAna1
    _ lizard          Anolis carolinensis     Feb 2007, anoCar1
    _ chicken         Gallus gallus           May 2006, galGal3
    _ frog            Xenopus tropicalis      Aug 2005, xenTro2
    _ fugu            Takifugu rubripes       Oct 2004, fr2
    _ tetraodon       Tetraodon nigroviridis  Feb 2004, tetNig1
    _ stickleback     Gasterosteus aculeatus  Feb 2006, gasAcu1
    _ medaka          Oryzias latipes         Apr 2006, oryLat1
    _ zebrafish       Danio rerio             Mar 2006, danRer4

These alignments were prepared using the methods described in the
track description file, multiz28way.html, based on the 
phylogenetic tree, 28way.nh.

The maf/chr*.maf.gz files each contain all the alignments to that 
particular human chromosome.  The multiz28wayAnno.tar.gz file
contains the same alignments for all chromsomes, 
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.

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/phastCons28way

---------------------------------------------------------------
To download a large file or multiple files from this directory, we recommend 
that you use ftp rather than downloading the files via our website. To do so: 
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg18/multiz28way

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  -  
[   ]28way.nh05-Jun-2007 12:00 468  
[TXT]multiz28way.html25-Jun-2007 14:04 20K 
[TXT]junk01-Nov-2007 13:28 322  
[   ]multiz28wayAnno.tar.gz10-Apr-2008 22:53 15G 
[TXT]README.txt24-Feb-2011 12:32 4.2K 
[DIR]alignments/10-May-2011 16:54 -  
[DIR]maf/10-May-2011 16:54 -  

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