The list of bioinformatics software tools can be split up according to the license used:

• List of proprietary bioinformatics software
• List of open-source bioinformatics software

Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on:

• Sequence analysis software
  • List of sequence alignment software
  • List of alignment visualization software
  • Alignment-free sequence analysis
  • De novo sequence assemblers
  • List of gene prediction software
  • List of disorder prediction software
  • List of Protein subcellular localization prediction tools
  • List of phylogenetics software
  • List of phylogenetic tree visualization software
  • Category:Metagenomics_software
• Structural biology software
  • List of molecular graphics systems
  • List of protein-ligand docking software
  • List of RNA structure prediction software
  • List of software for protein model error verification
  • List of systems biology modeling software
  • List of protein secondary structure prediction programs
  • List of protein structure prediction software
  • Category:Molecular dynamics software
  • Structural alignment software
• Other
  • Compression of genomic sequencing data
  • Bioinformatics workflow management system
  • List of biomedical cybernetics software
  • List of genetic engineering software
  • List of systems biology visualization software
  • List of systems biology modelling software
  • 2D gel analysis software
  • List of mass spectrometry software