Software
| 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 | http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/ | |||
| SylArray | Automated online analysis of miRNA seed enrichment | http://www.ebi.ac.uk/enright-srv/sylarray | |||
| MapMi | Automated mapping and analysis of miRNA sequences across genomes | http://www.ebi.ac.uk/enright-srv/MapMi |
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