Platform:
Ubuntu Linux is probably the simplest platform to install it on since it has most
of the programs needed and it is already compiled and packaged. Ubuntu can be down-
loaded fro free from www.ubuntu.com. Just follow its instructions for installation
of operating system and depending packages.

First:
Install MySQL database 5.0 or later and all dependencies listed at the website. 
All scripts are called from the BASH prompt. Grant the database to a username 
and a password that has to match the scripts called with database dependencies.

MySQL:
Load the example database and set passwords for access by the calling python and 
perl scripts. In the database there are examples of seven Rickettsia that 
immediately can be viewed with the script 'spacers/python/space7.py'. If you want 
to start a new project dump all data in all tables and run the 
'spacers/set_up_project.pl' script with your genomes in fasta format.

Inserting genomes:
The main script for inserting genomes for analysis to the database is by the script 
'spacers/set_up_project.pl' and the format for genomes is fasta. First argument is 
a project name and then any number of genomes. The genomes should be in the 
directory '/spacers'. Follow the examples in the script.

Visualization:
The script 'spacers/python/space7.py' let you view orfs of the genome and spacers 
between genes. It is possible to save the canvas with buttons.

Substitution frequencies:
The script 'spacers/python/kaks2core5.py' calculates Ka/Ks by PAML YN00, change 
relevant parameters directly in the script.