- bwa - Burrows-Wheeler Alignment Tool for efficient short read alignment - see 
- Cytoscape - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
EMBOSS - Hundreds of useful, well documented applications for molecular sequence and other analyses.
- FASTX-Toolkit - Command line tools for Short-Reads FASTA/FASTQ files preprocessing - see 
- GENtle - DNA restriction analysis and cloning tool similar to VectorNTI
- 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.
- NCBI C Toolkit - NCBI libraries and tools for biology applications srpm here
- NCBI C++ Toolkit - a new generation of NCBI libraries and tools for biology
- pyQPCR - qPCR analysis tool
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.