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    CGAT (Comparative Genome Analysis Tool)
           The source code distribution
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Reference:
    Uchiyama, I., Higuchi, T., Kobayashi, I.
    CGAT: a comparative genome analysis tool for visualizing alignments
    in the analysis of complex evolutionary changes between closely
    related genomes
    BMC Bioinformatics (in press)

Questions and comments should be sent to:
    Ikuo Uchiyama (uchiyama@nibb.ac.jp)

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Please see the project home page for the latest version:
    http://mbgd.genome.ad.jp/CGAT/

An online manual is available on this page.

You can find the equivalent (but possibly older) information
under this distribution at
    htdocs/CGAT/index.html

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   Quick Installation guide
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Requirements:
  You need at least Perl (5.8 or later), Java (1.4 or later), Ant
  and NCBI BLAST 2.x.

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   Quick guide for installation of the server package

1) SetUp.pl
   [confirm the CGAT_HOME directory and press the return key]
2) source etc/cgat.csh

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   Quick guide for web server setup

1) ln -s $CGAT_HOME/htdocs/CGAT ~/public_html
   (if you have a personal web page in the ~/public_html directory)
   (In this case, the Server URL is "http://MACHINE_ADDR/~USERNAME/CGAT/")

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   Quick guide for construction of the database

1) Prepare your genome data, or skip this step if your sequences
   are already in the MBGD database
2) Edit etc/speclist to specify the pairs of genomes to be compared
3) cd build
   BuildAll.pl
4) Release .pl

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   Quick guide for compilation of the client program

1) cd client
2) ant
3) Copy the dist/AlignmentViewer.jar file into an appropriate directory

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   Quick guide for setup of the client program to use your local server

1) java -Xmx512m -jar AlignmentViewer.jar
2) File=>Properties
3) Enter the server url (http://MACHINE_ADDR/~USERNAME/CGAT/ in the above
   example) in the Server URL field, press 'Add' and press 'OK'.
4) Select File=>Load and choose Server URL.

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   Quick guide for setup of the client program to load data from the local file

1) java -D$CGAT_HOME -Xmx512m -jar AlignmentViewer.jar
2) File=>Properties
3) Confirm the CGAT_HOME variable is correctly set.
   Otherwise, enter the correct one.
   Press 'OK'.
4) Select File=>Load and choose alignment data that does not have a
   '(Server)' statement.
