Installation and initial run

Download Gegenees

The software can be downloaded from There are several variants uploaded, depending on your operating system (OS). Windows. Macintosh and Linux are supported. You must also chose the correct processor architecture (32 bit or 64 bit).

To see architecture of your computer:

Java needs to be installed. You may check your Java version at this link:

Download and extract the compressed Gegenees program. Then run the Gegenees program from in the "Gegenees" folder.


Initial run

The first time Gegenees is started you will be asked to specify a "Workspace". This is the place where all your genomes and comparisons will be stored. Typically, a user always use the same workspace. Different users on the same computer might want to collect their genomes and comparisons in their own, separate workspace. The workspace can be changed by clicking “File” and "Switch workspace". The name of the current workspace can always be seen at the bottom left side of the "status line". The comparisons that are present in the current workspace will be listed in the table in the Workbench overview perspective.


Download BLAST+

If Gegenees starts OK, it is time to install BLAST+. It is recommended that Gegenees downloads and configure BLAST+ for you, but if you allready have BLAST+ installed or if you want to download and configure BLAST+ manualy, it is also ok. If you want to use Gegenees for the BLAST+ installation, select “Software” and then click on "Download BLAST+". BLAST+ is then downloaded and installed in your Gegenees installation folder under the new directory /bin/blast/. This is the directory were Gegenees expects to find BLAST+.

Download BLAST

BLAST+ can also be manually downloaded from

In general, the latest version of BLAST+ is recommended and can be downloaded from


Manually configuring the BLAST path

This part is optional and only necessary if you dont want Gegenees to install BLAST+ automatically and you allready have BLAST+ installed somewhere on your computer, then you have to manually configure Gegenees to find the BLAST executibles. Open the preferences dialog by clicking "File" -> "Preferences" -> "Third-party software conponents". Then specify the full path name to the directory containing the BLAST+ executables and then click “OK”. E.g. Windows, C:\blast+\bin\ or Linux, \usr\local \blast\. Dont forget to check the BLAST+ check box. This is necessary since Gegenees is also compatible with the older BLAST version blastall.

Download BLAST

If BLAST+ is added to your system path, you may not need to specify the path in the preferences.