InMoDe

by Ralf Eggeling, Ivo Grosse, and Jan Grau.

InMoDe is a collection of seven tools for learning, leveraging, and visualizing intra-motif dependencies within DNA binding sites and similar functional nucleotide sequences.

For a detailed description of the functionality of InMoDe see the user guide.

Paper

If you use InMoDe, please cite

R. Eggeling, I. Grosse, and J. Grau. InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites. Bioinformatics, 2017; 33(4): 580-582. doi: 10.1093/bioinformatics/btw689

Download and installation

InMoDe offers three user interfaces.

• InMoDeGUI.jar -- graphical user interface (version 1.1)
• InMoDeCLI.jar -- command line interface (version 1.1)
• InMoDeGalaxy.jar -- for integration into own Galaxy instance (version 1.1)

that can be started by

java -jar filename.jar

and require an existent Java installation (8u74 or later).

In addition, there are two user-friendly alternatives for installing the GUI variant of InMoDe (version 1.0), namely (i) a DMG for installation under Mac OS X, and (ii) a Windows installer.

Both do not require a recent Java, as they automatically install the required libraries to the local machine.

Webserver

A server with all tools of InMoDe (version 1.0) is available for public use at [1]. The provided web-server puts a certain limit on the complexity of runnable jobs for the learning tools. For unlimited use, please download InMoDe and install it to your local machine or own Galaxy instance.