External programs that can be used with MotifLab

Name Type Availability
AlignACEMotif discovery
BioProspectorMotif discovery
ChIPMunkMotif discovery
CloverMotif scanning
ClusterBusterModule discovery
CreateBackgroundModelModel creation
EMDEnsemble prediction
FIMOMotif scanning
MATCHMotif scanning
MDscanMotif discovery
MEMEMotif discovery
ModuleSearcherModule discovery
MotifComparisonMotif comparison
MotifLocatorMotif scanning
MotifLocator (old version)Motif scanning
MotifSamplerMotif discovery
MotifSampler (old version)Motif discovery
MotifScannerMotif scanning
PriorityMotif discovery
SeSiMCMCMotif discovery
WeederMotif discovery
Weeder2Motif discovery

The table above lists programs that are currently supported by MotifLab and have been tested and confirmed to work on at least one operating system. The download icons (blue arrows) link to XML-based configuration files that MotifLab needs in order to communicate with these programs. To use any of the programs, click on a link and save the file. Then start up MotifLab and select the "External Programs..." option in the "Configuration" menu. In the dialog that appears, click on the "Add Program from Configuration File" button and select the file you just saved. Note that all of these configuration files are also available in MotifLab's "External programs repository", so you can access them directly from within MotifLab by clicking the "Add Program From Repository" button instead (which is much easier). When you have selected the configuration-file in MotifLab (or selected a program for installation in the repository), MotifLab will begin the installation process. Unless the program you have selected is a "bundled" program (which means it is shipped as part of MotifLab itself), the program must already be installed on your own computer and you must tell MotifLab the location of the program. However, in some cases MotifLab might know where precompiled versions of the programs can be obtained and it will then be possible to download and install the program automatically. The "availability" column in the table above shows for which operating systems MotifLab can obtain the program for you. (If the OS icon has a mark on it, it means that the program has been tested on this OS. If it has not been tested, then we really can not guarantee that the downloaded program will work properly. Please inform use if you have any problems.) If your operating system is not listed in the "availability" column, then you will have to obtain the program yourself from somewhere on the internet and usually also compile the program yourself from the source code.

Other programs

The following table lists programs that have been considered for use with MotifLab but are not currently supported (for various reasons).
Name Status
ANN-Spec Not been able to acquire program or source code
Consensus Program will be supported in the next release of MotifLab
DME Not been able to successfully compile source code
Gibbs Motif Sampler Might be supported in future releases
GLAM2 Program allows INDELS in motifs and this is currently not supported by MotifLab
Improbizer Not been able to successfully compile source code
MITRA Not been able to acquire program or source code
NestedMICA Not been able to successfully compile source code
SMILE Uses a configuration file to specify parameter settings and this is currently not supported by MotifLab
SPACE Requires input files to be in a specific directory.
Trawler Not been able to successfully compile source code