This directory contains compressed FASTA alignments for the CDS regions
of the C. elegans genome (ce6, May 2008) aligned to the 
following assemblies:

  - C. remanei      May 2007, caeRem3      chain net
  - C. briggsae     Jan 2007, cb3          chain net
  - C. brenneri     Feb 2008, caePb1       chain net
  - C. japonica     Mar 2008, caeJap1      chain net
  - P. pacificus    May 2007, priPac1      chain net

Files included in this directory:
  - sangerGene.exon*.fa.gz: for each exon in the ce6 WormBase Gene track, this
    file contains either amino acids (AA) or nucleotides (Nuc) for ce6 and the
    aligning genomes.
  - refGene.exon*.fa.gz: for each exon in the ce6 RefSeq Gene track, this file 
    contains either amino acids (AA) or nucleotides (Nuc) for ce6 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/ce6/multiz6way/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.