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  A execution environment for the CoreAligner program.
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[1] Installation

Before executing the program, you might need to install the following
Perl libraries in your machine.

    PostScript::Simple    to make a PostScript file.
    LWP perl module       to download data from MBGD.

[2] Execute the examples

The following directories contain the dataset used in the paper
(I. Uchiyama, BMC Genomics, 9:515, 2008).

    data.bac: Bacillaceae dataset.
    data.ent: Enterobacteriaceae dataset.

Run the ExecAll script to execute these examples.


[3] Using CoreAligner with your own genomic data

You can run the program against any set of genomes provided that they
are included in the MBGD database. First, you should create an
ortholog table on MBGD as follows:

  1) Access the MBGD top page (http://mbgd.genome.ad.jp/).
  2) Click "Create/View Ortholg Table"
  3) Choose a set of organisms to compare, and press "Create/View
     Cluster Table" button. 
  4) After the result is returned, press "Save Complete Table" button
     to save the resulting table.

Create a directory and put the above saved file in it. Copy
"data.bac/param.ph" file into this directory and edit it
appropriately (mandatory).  Then, run "script/exec_all.pl" script
to execute the program as follows:

../script/exec_all.pl $(SAVED_DIR)/$(SAVED_FILE)

The following files are created in $(SAVED_DIR).

corealign.out: text output showing the consensus order of ortholog
group included in the core structure.

corealign.ps: PostScript file showing a graphical view of the
core alignment.

[4] Using CoreAligner through the RECOG system

Alternatively, probably you can better use the program through the
RECOG system (Research Environment for Comparative Genomics)
that includes CoreAligner as a built-in function.
See http://mbgd.genome.ad.jp/RECOG/.
