Name Description Binary Source GPL Implementation
BioLayout Biological Network Visualisation and Analysis X     Java 1.4
BioLayout Express 3D Biological Network Visualisation and Analysis X X X Java 1.5, OpenGL
CAST Low-complexity sequence filter X X   ANSI C
GeneRAGE Protein Sequence Clustering and Domain Decomposition X     ANSI C
miRanda MicroRNA Target Detection in 3' UTRs X X X gcc/autoconf
MCL Markov Clustering X X X gcc/autoconf
Sylamer Analysis of enrichment or depletion of motifs and words in ordered genelists X X X gcc/autoconf (Java 1.5 GUI)
Kraken Quality control and analysis of high-throughput sequence data X X X C, R, perl

Databases and web services

Name Description URL
MicroCosm Targets microRNA Sequences, Registry and Targets
SylArray Automated online analysis of miRNA seed enrichment
MapMi Automated mapping and analysis of miRNA sequences across genomes

Chimira Analysis of small RNA Sequencing data and microRNA modifications.