This directory contains compressed FASTA alignments for the CDS regions
of the C. elegans genome (ce9, Jan. 2010) aligned to the 
following assemblies:

  - Caenorhabditis elegans                Jan. 2010  ce9/WS210
  - Caenorhabditis briggsae               Jan. 2007  cb3/WS210/WUGSC 1.0
  - Caenorhabditis remanei                May  2007  caeRem3/WS210/WUGSC 15.0.1
  - Caenorhabditis brenneri               Feb. 2008  caePb2/WS210/WUGSC 6.0.1
  - Caenorhabditis japonica               Sep. 2010  caeJap3/WUGSC 7.0.1
  - Haemonchus contortus                  Dec. 2009  haeCon1/WS210
  - Pristionchus pacificus                Dec. 2008  priPac2/WUGSC 5.0.1
  - Meloidogyne hapla VW9                 Sep. 2008  melHap1/WS210
  - Meloidogyne incognita                 Feb. 2008  melInc1/WS210
  - Brugia malayi                         Sep. 2007  bruMal1/WS210/TIGR 1.0

Files included in this directory:
  - sangerGene.exon*.fa.gz: for each exon in the ce9 WormBase Gene track, this
    file contains either amino acids (AA) or nucleotides (Nuc) for ce9 and the
    aligning genomes.
  - refGene.exon*.fa.gz: for each exon in the ce9 RefSeq Gene track, this file 
    contains either amino acids (AA) or nucleotides (Nuc) for ce9 and the 
    aligning genomes.

For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html 
and http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FASTA.

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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/ce9/multiz10way/alignments/

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.