GeneNet Toolbox for MATLAB

View the Project on GitHub avigailtaylor/gntat14

GeneNet Toolbox for MATLAB - Download Page

Please use one of the buttons above to download a copy of GeneNet Toolbox.


If you have any questions or comments regarding GeneNet Toolbox, please email with the subject line "GeneNet Toolbox".

IMPORTANT: Please note that the email address provided in the corresponding Bioinformatics paper (see citation information below) is no longer active.


GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks

Avigail Taylor; Julia Steinberg; Tallulah Andrews; Caleb Webber

Bioinformatics 2014;

doi: 10.1093/bioinformatics/btu669

System Requirements

Option 1 – Using GeneNet Toolbox in a MATLAB Environment

Running GeneNet Toolbox in a MATLAB environment requires at least MATLAB 2013B and Perl. No compilation is required. The toolbox can be used on any computer where MATLAB and Perl are installed, and is therefore available for Windows, Linux, and MAC OS machines.

Option 2 – Using GeneNet Toolbox Tools as Standalone Applications

GeneNet Toolbox tools are also available as a set of standalone applications that can be run in a Linux environment. Perl must be installed. Running these applications requires installation of the MATLAB Compiler Runtime (version R2013b (8.2)), which is freely available from You do not need a MATLAB licence to run these GeneNet Toolbox standalone tools. No compilation is required.

Download and Installation

Option 1 – MATLAB Environment

Using the buttons at the top of this page, download the ZIP file or the TAR ball, unzip/ extract the download, and save the whole genenet directory (folder) in your favourite directory for your MATLAB downloads. The genenet directory contains everything you need to run GeneNet Toolbox and the Network Permutation Analyser. To install GeneNet Toolbox you need to set the MATLAB path to include the full path to where you have saved the genenet directory. The easiest way to do this is to start MATLAB, then using the MATLAB desktop:

  1. In the ‘HOME’ tab, under ‘ENVIRONMENT’, click ‘Set Path’.

  2. In the ‘Set Path’ dialogue box that comes up, click the ‘Add with Subfolders...’ button.

  3. A file selection dialogue box will appear; use this to navigate to the genenet directory. Highlight the genenet directory, and then click ‘Open’.

  4. Click ‘Save’ in the ‘Set Path’ dialogue box.

You are now ready to use GeneNet Toolbox!

Option 2 – Standalone Tools

Using the buttons at the top of this page, download the ZIP file or the TAR ball, unzip/ extract the download, and save the genenet_standalone directory in your favourite directory for applications. To install GeneNet Toolbox standalone tools, carry out the following steps:

  1. Open a terminal

  2. cd to the genenet_standalone directory

  3. You need to change the permissions on all of the *.sh files, so that they can be executed. Type the following at the prompt, then press return: chmod +x *.sh

If you do not have a copy of the Linux 64-bit version of the MATLAB Compiler Runtime (MCR), download it from Mathworks by navigating to:

Save the downloaded file to the genenet_standalone directory, return to the terminal opened above, and type the following at the prompt (press return after each statement):


cd MCR_R2013b_glnxa64_installer


Follow the installer instructions. (IMPORTANT: During the installation you will be asked to choose a directory in which to install the MCR. Make a note of the full path of this directory. When you run the standalone tools you will need to know the mcr_directory. This is: full_path_to_mcr_install_directory/v82).

You are now ready to use GeneNet Toolbox standalone tools!