- bwa - Burrows-Wheeler Alignment Tool.
- EMBOSS - Hundreds of useful, well documented applications for molecular sequence and other analyses.
- MIRA - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats.
- NCBI-BLAST and other tools - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
- SAMtools - SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.
- Staden - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Taverna - Tool for automation of experimental workflows.