Homograph has been tested on Windows XP. Be warned, it runs MUCH better under linux, so if you can, use the linux version instead.

Software requirements:
- ActivePerl

1) Make sure you have ActivePerl installed.

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

PROGRAM:

homograph.zip (34 kb)

DATABASES:

Organisms (# of)	zip format (size)
Archaea (16)	archea.zip (7.1 mb)
Eukaryotes (5)	eukarya.zip (17 mb)
Firmicutes (31)	firmi.zip (34 mb)
Gamma proteobacteria (21)	gamma.zip (29 mb)
Enterobacteriaceae (10)	entero.zip (11 mb)
All organisms (105)	all.zip (369 mb)

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

If you can't open a zip file, download winzip

4) The Homograph package, upon extraction, will create a Homograph/ subdirectory. To run Homograph simply go into this directory and double-click on ./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.zip (3007 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.zip (1737 kb)