Download MotifLab v2.0  (pre-release version 2.0.-1. Requires Java 1.7)


Last updated: 2016–08–10

Note that version 2.0 of MotifLab is still in pre-release stage and not all of the promised functionality has been implemented yet!


Launch MotifLab   (Java Web Start)

256MB 512MB 1GB 2GB 4GB

Launch MotifLab with minimal GUI

256MB 512MB 1GB 2GB 4GB


Download MotifLab for local installation

Download ZIP


If you experience problems with resolving gene identifiers in the "Add Sequences" dialog, you might have to update your configuration files. Download the two files below and install them by selecting "Install Configuration File..." from the "Configure" menu. (If you have made any changes to the configuration you should consider using the "Backup Configuration Files..." option first).



New features in MotifLab v2

Version 2.0 of MotifLab does not really look that much different from previous versions, nor does it include many new operations or analyses.
The main focus of the new version is to improve the performance of the existing functionality (especially when working on larger datasets) and also to make the program more flexible and configurable.


Some highlights of version 2.0 include:
  • Easier to configure new organisms and data sources
  • More options for loading feature data from SQL databases or local files (BigBED, BigWIG or 2bit)
  • Faster and more responsive GUI, especially when visualizing many sequences
  • Improved performance of UNDO/REDO system and local data caching
  • Support for Excel formats for input and output
  • New data type: General Maps (that can contain text values rather than just numeric values)
  • The GUI now includes a "Sequence Browser" tool to list all sequences and filter sequences based on properties (analogous to the Motif Browser and Module Browser tools).
  • Possibility to annotate Sequence objects with additional properties, including GO annotations
  • Support for long-range chromatin interaction data
  • Possibility to define macros to use in protocols
  • A plugin system that allows MotifLab to be easily extended with new features
(Note that not all of these features are currently available)