Click here to download the latest version (v1.9) of Gene Stacker. Some example input files, among which the one discussed on the example page, are included in the package. Previous versions are also available below.

Latest release
v1.9 28 August 2015 Download
Previous versions
v1.8 21 January 2015 Download
v1.7 06 January 2015 Download
v1.6 10 September 2014 Download
v1.5 17 March 2014 Download
v1.4 06 December 2013 Download
v1.3 20 November 2013 Download
v1.2 23 September 2013 Download
v1.1 20 August 2013 Download
v1.0 13 August 2013 Download

R Interface

The downloadable package also includes a wrapper script genestacker.R to run Gene Stacker from R. See the usage page for instructions on how to use this interface.


Gene Stacker is implemented in Java and requires a Java Runtime Environment (JRE 7 or higher), available for download here. To produce visualizations of the constructed crossing schedules, Gene Stacker relies on the Graphviz software, which can be freely obtained here.


The CLI is ready to use and does not require installation, see the usage page for instructions. When running Gene Stacker for the first time, a config file named will be created in your home directory under ~/genestacker/. It has the following structure:

# Genestacker config file

# Absolute path to the dot command line tool,
# e.g.:
# dot.path=/usr/bin/dot                                     (Linux)
# dot.path=/usr/local/bin/dot                               (Linux)
# dot.path=C:/Program Files/Graphviz2.32/bin/dot.exe        (Windows)
# dot.path=C:\\Program Files\\Graphviz2.32\\bin\\dot.exe    (Windows)

# location of crossing scheme XML Schema

# location of genestacker input XML Schema
This file can be edited using your favorite text editor (on Windows, Notepad may show everything on a single line, use another text editor like WordPad to avoid this). Usually, only the dot.path entry should be adjusted to the absolute path of the dot command line tool, which comes with the Graphviz software. For Unix operating systems, after installing Graphviz, open a terminal window and type
$ which dot
to find out where the dot command has been installed, in our case in /usr/local/bin/dot. On Windows, the dot.exe executable is located in the bin directory of the Graphviz installation folder, which can be specified when installing Graphviz. By default, the path will be
C:\Program Files\Graphviz[VERSION]\bin\dot.exe
where [VERSION] should be replaced with the appropriate version number. Note that in the Gene Stacker config file, you should either use forward slashes or double backslashes as separator in Windows paths, for example
C:\\Program Files\\Graphviz2.32\\bin\\dot.exe
C:/Program Files/Graphviz2.32/bin/dot.exe
If Graphviz is not installed, or if the correct path to the dot command is not set in the config file, Gene Stacker will not produce visualizations of the constructed crossing schedules. Such visualizations can then be generated afterwards based on the output files, see the output section of the usage page for more details.