This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/multiz13way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the Marmoset genome (calJac3, March 2009):

  - marmoset        Callithrix jacchus      Mar 2009, calJac3  reference
  - human           Homo sapiens            Feb 2009, hg19     chain nboon
  - Baboon          Papio hamadryas         Nov 2008, papHam1  recip best
  - Bushbaby        Otolemur garnettii      Dec 2006, otoGar1  recip best 
  - Chimp           Pan troglodytes         Mar 2006, panTro2  chain net
  - Dog             Canis lupus familiaris  May 2005, canFam2  chain net
  - Gorilla         Gorilla gorilla gorilla Oct 2009, gorGor2  recip best
  - Mouse           Mus musculus            July 2007, mm9     chain net
  - Opossum         Monodelphis domestica   Oct 2006,  monDom5 chain net
  - Orangutan       Pongo pygmaeus abelii   July 2007, ponAbe2 chain net
  - Rhesus          Macaca mulatta          Jan 2006,  rheMac2 chain net
  - Mouse lemur     Microcebus murinus      Jun 2003,  micMur1 recip best
  - Tarsier         Tarsier syrichta        Aug 2008,  tarSyr1 recip best

These alignments were prepared using the methods described in the
track description file, multiz13way.html, based on the 
phylogenetic tree, 13way.nh.

The calJac3.13way.maf.gz file contains all the alignments to the 
Marmoset contigs, with additional annotations to indicate gap context.

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 
marmoset, 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 marmoset; 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/calJac3/phastCons13way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/phyloP13way

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=calJac3&g=cons13way

---------------------------------------------------------------
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/calJac3/multiz13way

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.