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.
InMoDe is continuously developed further. Feel free to report bugs, make feature requests, or give other comments and suggestions to eggeling[at]cs.helsinki.fi. If you wish to be notified about news regarding the software, such as releases of a next version, send an email with the header "InMoDe subscribe" to the aforementioned address.
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 -- graphical user interface
- InMoDeCLI -- command line interface
- InMoDeGalaxy -- for integration into own Galaxy
that can be started by
java -jar filename.jar
and require an existent Java installation (8u74 or later).
Both do not require a recent Java, as they automatically install the required libraries to the local machine.
A server with all tools of InMoDe is available for public use at galaxy.informatik.uni-halle.de. 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.
- InMoDe User Guide (version 1.1)
- Source code