External programs that can be used with MotifLab

Name	Type		Availability
AlignACE	Motif discovery
BioProspector	Motif discovery
ChIPMunk	Motif discovery
Clover	Motif scanning
ClusterBuster	Module discovery
CreateBackgroundModel	Model creation
EMD	Ensemble prediction
FIMO	Motif scanning
MATCH	Motif scanning
MDscan	Motif discovery
MEME	Motif discovery
ModuleSearcher	Module discovery
MotifComparison	Motif comparison
MotifLocator	Motif scanning
MotifLocator (old version)	Motif scanning
MotifSampler	Motif discovery
MotifSampler (old version)	Motif discovery
MotifScanner	Motif scanning
Priority	Motif discovery
SeSiMCMC	Motif discovery
Weeder	Motif discovery
Weeder2	Motif 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