Beta testing of Gegenees Fragmented Aligner version 3.0

This is a beta-version for testing functionality. Please look for updates at and report any problems to or



Download the windows version of Gegenees-FA. If you have a 64-Bit environment, download the ”x_86_64” version and if you have a 32-bit environment download the ”x86” version. Note, even if you have a 64-bit windows version, the java version may be 32-bit. To check this: Open a command prompt (search for cmd in the windows menu) and type ”java -version”. If java is installed a version will be reported. The java version must be 1.8.x or higher. If the java version is 64-bit, there should be a statement about ”64-Bit” somewhere in the version information. If java stops and returns ”exit code 13” when you try to start Gegenees-FA, you are probably trying to run a 64-bit Gegenees version using a 32-bit Java version. Gegenees-FA is started by double-clicking the Gegenees-FA program located under the eclipse folder.

64 bit version windows:  (build 2017-10-12)

32 bit version windows (not tested):  (build 2017-10-12)


Download the Macintosh version of Gegenees-FA. Gegenees-FA requires java version 1.8.x or higher. Note, on macintosh the commandline version of java is not always the same as the graphical version. Gegenees uses the command line version. To check your java version, open a terminal window and type ”java -version”. If java is installed in the command line environment, version information will be displayed. The version must be 1.8.x or higher. If you need to install or update your command line version of java, download and install the latest Java Development Kit (JDK) version. Note, it must be the JDK version, not the JRE version for it to become accessible from the command line. Gegenees-FA is started by double-clicking the Gegenees-FA executable file in the MacOS folder. Eventually you need to open it by right clicking (ctrl-clicking) and explicitly allowing it to be run.

Macintosh version:   (build 2017-10-12)


The first Linux version is nor released for beta-testing. Gegenees-FA requires java version 1.8.x or higher. Type ”java -version” in a terminal to check. Start the program by double clicking Gegenees in the eclipse folder. If it does not start, check that the launcher is marked as beeing allowed to execute.

Linux version (64-bit): linux.gtk.x86_64.tar.gz   (build 2017-10-12)

Linux version (32-bit) (not tested): linux.gtk.x86.tar.gz   (build 2017-10-12)


User manual draft   (build 2017-10-12)

Update history log

Full list of changes

2017-10-12: GBK import bug-fixed.
2017-09-13: New version WIN + MAC + LNX (64-bit) uploaded.
2017-09-06: First betaversion WIN + MAC uploaded.