- Autodock - Suite of automated molecular docking tools
- Autodock Vina - Tool for drug discovery, molecular docking and virtual screening
- COPASI - Simulation and analysis of biochemical networks and their dynamics, supports SBML standard for models
- Cytoscape - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
- FASTX-Toolkit - Command line tools for Short-Reads FASTA/FASTQ files preprocessing (Review Request)
- GENtle - DNA restriction analysis and cloning tool similar to VectorNTI
- Integrative Genomics Viewer - java-based graphical genomics viewer (licensed under GPLv2)
- 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
- 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.