Homograph has been tested on several different computers running:

Mandrake Linux versions 8-9
RedHat Linux versions 7-8

Software requirements:

- Perl
- Perl/Tk

1) Make sure you have Perl and Perl/Tk installed. Check these installation notes for Perl/TK at the bottom of the page.

2) Make a directory for Homograph and download the PROGRAM and at least one DATABASE file into it.

PROGRAM:

homograph.tar.gz (24 kb)

DATABASES:

Organisms (# of)	tar format (size)
Archaea (16)	archea.tar.gz (6.9 mb)
Eukaryotes (5)	eukarya.tar.gz (16 mb)
Firmicutes (31)	firmi.tar.gz (33 mb)
Gamma proteobacteria (21)	gamma.tar.gz (28 mb)
Enterobacteriaceae (10)	entero.tar.gz (10 mb)
All organisms (105)	all.tar.gz (357 mb)

3) Extract each and every one of the files you downloaded into the same directory with:

tar -zxvf filename

4) The Homograph package, upon extraction, will create a Homograph/ subdirectory. To run Homograph simply go into this directory and execute ./homograph.pl

Note: the Homograph/ directory also contains the manual, readme and paths (configuration) files. Remember to set your paths file correctly if you are using personalized databases.

Extra packages, containing lists of Files for all genomes to automatically view in Homograph:

COG classification, divided by Information storage/processing, Cellular processes, Metabolism and Poorly characterized/Not assigned: (example screenshot)
files-cogs.tar.gz (2777 kb)

High and low GC Skew at 3rd base positions, using a sliding window equivalent to a 50th of the genome's size. These can be used to locate origin of replication: (example screenshot)
files-gc_skew.tar.gz (1693 kb)

Installing Perl/Tk:

To check if you have Perl/Tk installed type the following in a console:

perl -e "use Tk"

If nothing happens, Perl/Tk is already installed. You will need to install Perl/Tk if you get an error like:

Can't locate Tk.pm in @INC (@INC contains: /usr/lib/perl5/5.6.1/i386-linux /usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/i386-linux

First download the Perl/Tk module from CPAN. Then (considering you downloaded Tk-800.024.tar.gz), you will need to do the following to compile and install:

tar -zxvf Tk-800.024.tar.gz
cd Tk800.024
perl Makefile.PL
make
make test
make install

Only the last step (make install) requires that you be root.