This directory contains compressed multiple alignments of the 
following assemblies to the C. elegans genome (ce6, May 2008):

  - C. remanei      May 2007, caeRem3      chain net
  - C. briggsae     Jan 2007, cb3          chain net
  - C. brenneri     Feb 2008, caePb2       chain net
  - C. japonica     Mar 2008, caeJap1      chain net
  - P. pacificus    May 2007, priPac1      chain net

These alignments were prepared using the methods described in the
track description file multiz6way.html, based on the phylogenetic tree 6way.nh.

The ce6.6way.maf.gz file contains all the alignments to the 
C. elegans contigs with additional annotations to indicate gap context.

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 
C. elegans, 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 C. elegans; 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/ce6/phastCons6way.

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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/calJac1/multiz9way

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.

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      ce6.6way.nh             2008-06-09 15:44  195   
      chrM.maf.gz             2008-06-19 14:20   22K  
      chrX.maf.gz             2008-06-19 14:20   21M  
      chrII.maf.gz            2008-06-19 14:20   17M  
      chrIII.maf.gz           2008-06-19 14:20   15M  
      chrIV.maf.gz            2008-06-19 14:20   18M  
      chrI.maf.gz             2008-06-19 14:20   16M  
      chrV.maf.gz             2008-06-19 14:20   22M  
      md5sum.txt              2008-10-16 12:17  372   
      alignments/             2011-02-23 17:23    -   
      maf/                    2019-11-06 10:43    -