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 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 genetic engineering software
    • List of systems biology visualization software
    • List of systems biology modelling software
    • 2D gel analysis software
    • List of mass spectrometry software
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