- SAMtools - SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
- bwa - Burrows-Wheeler Alignment Tool
- EMBOSS package - Hundreds of useful, well documented applications for molecular sequence and other analyses.
- Staden package - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- NCBI-BLAST and other tools - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.