Motif
- Network Motif Clustering Toolbox 2.0 – Cluster Topological Network Motif
- MIM – Motif Independent Metric
- Gibbs Motif Sampler 3.10 – Identify Motifs, Conserved Regions, in DNA or Protein Sequences
- Protein Sequence Motif Extractor 1.0.4752 – Look for the specified Motif in each Protein Sequence
- MEME 4.9.0 – Discovering Motifs within the Sequences
- DIAL – 3-Dimensional RNA Structural Alignment and Motif Detection
- sMotif / exMotif – Extract / Mine Structured Sequence Motifs DNA sequences
- POSMO v2 – Motif Discovery tool
- AhoPro – Seach for Overrepresentation of Given motifs in DNA sequences, P-value calculation
- ProSMoS – Protein Structure Motif Search
- RISOTTO – Motif Discovery Tool
- GRISOTTO – Motif Discovery Tool
- Sequence Searcher – Search Sequences for Specified Sequence Motifs
- DIPS 1.1 – Dind Discriminative PWM Motifs
- PhyME – Find Motifs in sets of Orthologous Sequences
- Voting 4 – Discover Patterns, Motif, in a set of DNA sequences
- Clover 20120216 – Find Overrepresented Motifs in DNA Sequences
- Compo – Composite Motif Discovery
- TAMO 20120321 – Analyze Transcriptional Regulation using DNA-sequence Motifs
- MAVisto 2.7.0 – Motif Analysis and VISualisation TOolkit
- ReMoDiscovery – Inferring Transcriptional Module networks from ChIP-chip-, motif- and microarray data
- RNAmotifs 3 – Predict a motif for your own set of RNAs
- FMM 2 – Learn Motifs from Unaligned Sequences
- MotifDetector – Finding Motifs in Multiple DNA sequences
- DRIM – Discover Motifs in a list of ranked DNA sequences
- Alien_hunter 1.7 – Interpolated Variable Order Motifs for Identification of Horizontally Acquired DNA
- Mapwhere 1.0 – Finds Perfect or Partial Matches to Motifs
- FANMOD 20061223 – Fast Network Motif Detection.
- motifdraw – Graphically Represent Motifs
- RISO – Motif Discovery Tool
- MotifOrganizer 0.1 Beta – Cluster large sets of DNA sequence motifs to identify common patterns
- HMS 0.1 – Hybrid Motif Sampler
- SMAP 2.0 – Comparison & Similarity Search of Protein Three-dimensional Motif
- FoldMiner 200312 – Structural Similarity Searches and Motif Discovery
- 3MATRIX 1.0 – Motif in 3D
- 3MOTIF 2.0 – Motif in 3D
- EMOTIF 3.6 – Sequence Analysis Using Pareto-optimal Discrete Motifs
- MotifRegressor – Find DNA Sequence Motifs
- MDScan 2004 – Find Motif from ChIP-on-chip Targets
- LocalMotif 1.0 – Discover Transcription Factor Binding Motifs
- ALIDOT 2.0.5 – Detect Conserved Secondary Structure Motifs
- RNAMotif 3.0.7 – Find Structural Motifs in RNA
- RNASampler 1.3 – Predict RNA Secondary Structure Motifs
- YMF 3.0 /FindExplanators 1.1.3 – Finds Short Motifs in DNA Sequences
- ROVER 20050711 – Find Relatively Overrepresented Motifs in DNA Sequences
- Cister – Find Motif Clusters in DNA Sequences
- COMET – Cluster Of Motifs E-value Tool
- Cluster-Trainer 20071204 – Estimates Optimal Motif Weights for Cluster-Buster
- Cluster-Buster 20100219 – Find Dense Clusters of Motifs in Nucleotide Sequences
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