| CAP3 | A sequence assembly program to assemble sequence segments into overlapping sequences (useful for creating contigs from ESTs, for instance). |
| CD-HIT | CD-HI/CD-HIT are programs for clustering large protein database at high sequence identity threshold. |
| Clustal Series | A series of multiple sequence alignment programs for DNA or proteins. |
| Crover | A software framework to support the development
of Bioinformatics tools and applications. |
| fastacmd | Retrieves FASTA formatted sequences from a blast database. |
| GENSCAN | A gene identification program which analyzes genomic DNA sequences. |
| HMMER | A biological sequence analysis tool using profile hidden Markov models (HMMs). |
| HMMTOP | Predicts both the localization of helical transmembrane segments and the topology of transmembrane proteins using hidden Markov model (HMM).
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| ProperTM | ProperTM is a web service that calculates properties associated with positions in a sequence alignment. |
| ProKink | A program to measure the geometry of proline kinks in a simulation trajectory
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| PSIPRED | A protein secondary structure prediction tool based on position-specific scoring matrices. |
| Pseudoknots | Pseudoknots (or RNAfold_knots) is an extension of the Zuker MFOLD algorithm to optimize the minimum energy prediction of pseudoknotted RNA structures. It can also include coaxial energy information. |
| RbDe | A web service allowing the iterative construction of
residue-based diagrams of proteins. |
| RbDg | RbDg is a program that generates residue-based diagrams of proteins. RbDg can be thought of as a batch version of RbDe with added features. |
| Seqinfo | A utility which can be used to rapidly summarise output from the BLAST suite of programs. |
| T-Coffee | A multiple sequence alignment package, which provides a dramatic improvement in accuracy over ClustalW. |
| Textactor | Textractor is a software framework designed to facilitate the development of software tools that process text to extract information.
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| TissueInfo | A series of tools to predict
the tissue distribution of genes and EST (knowledge-based prediction).
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