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- 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
* Bioinformatics workflow management system
* List of genetic engineering software
* List of systems biology visualization software
* List of systems biology modelling software
*
* List of mass spectrometry software (en)
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- 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: (en)
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- List of bioinformatics software (en)
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