Simulation
- CoalFace 0.3b – Simulation of the Coalescent Process with the visual display of Gene Genealogies
- YASARA 13.4.21 – Molecular Graphics, Modeling & Simulation program
- FASIMU 2.3.3 – Flux-balance Analysis based SIMUlations
- HEC 0.2 – Haploid Simulation of Bacterial Communities
- VCell 5.1 – Environment for Modeling & Simulation of Cell Biology
- GNU MCSim 5.5.0 – Simulation & Statistical Inference Tool
- OpenMM 5.0.1 – Library for Molecular Modeling Simulation
- PhyloSim 2.0.1 – Monte Carlo Simulation of Sequence Evolution
- TESS 1.2.0 – Simulation of Reconstructed Phylogenetic Trees under Time-dependent Birth-death Processes
- Lattice Microbes 2.1 – Simulation method for the Reaction-diffusion Master Equation
- CPSIM – Genetic Maps & Markers Simulation
- PedigreeSim – Simulation of Genotypes in Pedigrees of Diploid and Tetraploid Species
- CellSys 5.0 – Cell-based Simulation software for Multi-cellular systems
- GROMACS 4.6.1 – Molecular Simulation
- CellMLCompiler 2.0 – Software Platform for Biological Function Simulation
- BioSimWare 201103 – Stochastic Modelling, Simulation and Analysis of Biological Systems
- MassXpert 3.4.0 – Polymer Chemistry Modelling & Simulation/Analysis of Mass Spectrometric Data
- Protein Purification 1.4 – Protein Purification Simulation for iPad
- GenePool 6 / Swimbots 1.0 – Artificial Life Simulation
- WinSAAM 3.0 – The Simulation, Analysis and Modeling Software
- ChemChains 1.22 – Simulation & Analysis of Logical Models
- CSim 20000614 – Simulation program for Somatic Cancer Evolution
- pDynamo 1.7.2 – Simulation of Molecular Systems
- MDWeb / MDMoby – Web-based Platform for Molecular Dynamics Simulations
- CES 1.0 – Codon Evolution Simulation
- hypred 0.2 – Simulation of Genomic Data in Applied Genetics
- Rosetta 3.4 – Simulation and Design of Protein
- GeneExplorer 2.1.0 – Simulation of Gene Expression
- VGLII 3.2.0 – Interactive Simulation of Mendelian Genetics
- Aipotu 1.3.2 – Simulation Linking Genetics, Biochemistry, Molecular Biology & Evolution
- popgen 0.1 – Population Genetic Simulations & Numerical Analysis
- Browndye 20120821 – Brownian Dynamics Simulations on Large Biological Molecules.
- GWAsimulator 2.1 – Rapid Whole Genome Simulation program
- RocketBugs / RocketBugsRender – Simulation of the Actin-based Motility of Listeria Monocytogenes
- ParMSpindle 1.0 – Simulation of the ParM mediated Segregation of Bacterial Plasmids
- Ingeneue 0.93b – Gene Network Simulation Software
- MDLab – Molecular Dynamics Simulation Prototyping Environment
- MCRobot 2.1 – Illustrates the basic principles of Markov chain Monte Carlo Simulation
- EvolSimulator 2.1.0 – Simulation Test Bed for Hypotheses of Genome Evolution
- ALF 1.0 – Simulation Framework for Genome Evolution
- SNaP – Simulation of sNp haplotype data And Phenotypic traits
- SIMCOAL 2.1.2 – Simulation of Molecular data in interconnected Populations with Arbitrary Demography
- Rmetasim 1.1.12 – METApopulation SIMulation
- FEST 0.0.6 – Simulations and Likelihood Calculations of Pair-wise Family Relationships
- PopBio 3.0.1 – Population Biology Simulation package
- FPG – Forward Population Genetic Simulation program
- MGA-SIMULATE – Simulation of Genotypes and Quantiative Phenotyps
- neuroants – Simulation of Ant Colony
- SimMLST 1.0 – Simulation of MLST data under a Neutral Model
- POPSIM 2.13 – Population Simulation program
- geneRegulationSimulation – Perform Simulations for Transcription Regulation Network
- SLINK 3.00 – Simulation program for Linkage Analysis
- PNK 2e – Modeling and Simulation of Biological Processes
- JigCell 7.1.0 – Modeling and Simulation software
- CS-PSeq-Gen 1.0 – Simulation of Protein Sequences under Constraints
- GNA 8.1 – Modelling & Simulation of Genetic Regulatory Networks
- Alfacinha – Simulation of Sequence Evolution with Neighbouring-site Dependencies
- MaSK 1.3.0 – Molecular Modeling and Simulation Kit
- ProtoMol 3.3 – Molecular Dynamics (MD) Simulation
- Bionet 3.0a – Biological Cell Network Pathway Simulation
- NAST 1.0 – Nucleic Acid Simulation Tool
- SIMLA 3.3 – SIMulation of Pedigree Data for Linkage and Association Studies
- SIBSIM 2.1.3 – Phenotype Simulation in Extended Pedigrees
- GASP 3.31 – Genometric Analysis Simulation Program
- CardioLab 3.0 – Simulation of in vivo Cardiovascular Pharmacology Experiments
- NeuroSim 4 – Neurophysiology Simulations
- PopG 3.3 – Genetic Simulation Program
- MESA 1.9.23 – Macroevolutionary Analysis & Simulation
- Protein Investigator 3.0.2 – Simulation of Protein Folding
- Diffusion Simulator – Simple Diffusion Random Walk Simulation
- mlcoalsim 1.42 – Multilocus Coalescent Simulations
- COSMOS 5.0 / COSMOS Viewer 3.0 – Computer Simulation & Visualisation of Molecular Structures
- Circadian Modelling 2.0 – Simulations using Mathematical Models of Biological Clocks
- 3D Cell Simulation & Stain Tool 2.0 – Learn about the Cell & all its Structures
- DarwinPond 2005 – Artificial Life Simulation
- GEvolutionS – Genome Evolution Simulation
- Bio-SPICE Dashboard 7.0 – Viological Simulation Program for Intra- & Inter-Cellular Evaluation
- Cellware 3.0.1 – Modeling & Simulation Tool for Modeling Cellular Transactions
- Gepasi 3.30 – Biochemical Kinetics Simulation
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