Simulator
- UNICOR 2.0 – Species Connectivity and Corridor Network Simulator
- phyloBreak – Gene Genealogy Simulator for Phylogeographic Study
- genePed 2.0 – Gene Genealogy Simulator based on Organismal Pedigree
- BottleSim 2.6 – Population Bottleneck Simulator
- Wessim 1.0 – Whole Exome Sequencing SIMulator using in silico exome capture
- Cellzilla2D 3.0 – Two-dimensional Tissue Objects Simulator
- AnA-FiTS 1.0.2 – Forward-in-time Simulator for Polymorphism data
- COPASI 4.9.45 – Biochemical Network Simulator
- PhyloGeoSim 1.0 beta – Phylogeographic Simulator
- MaCS 0.5b – Markovian Coalescent Simulator
- ShotGun 1.0.10 – Flexible Short Read Simulator
- Sherman 0.1.3 – Bisulfite-treated Read FastQ Simulator
- TESD 1.0 – Transposable Element Simulator Dynamics
- Pysces 0.8.0 – Python Simulator of Cellular Systems
- MCell 3.1.998 – Monte Carlo Simulator of Cellular Microphysiology
- TreesimJ 0.7 – Population Genetics Simulator Program
- Flow Cytometer Simulator – Simulation of a Working Flow Cytometer
- Meredys 20100209 – Multi-compartment Reaction-diffusion Simulator
- GSIM – Microarray Gene Expression Simulator
- Pensim 2.0 – Modularized Simulator for Penicillin Fermentation
- Ginkgo 3.9.0 – Phylogeographical Evolution Simulator
- Adun 0.81 – Biomolecular Simulator
- SIMULATOR 1.0 – Simulate DNA and Protein datasets with well-defined Insertion-deletion dynamics
- QMSIM 1.00 – Qtl and Marker SIMulator
- ggs – Grid Genotype Simulator
- Hapsample 0.12 – Association Simulator for Candidate Regions or Genome Scans
- Kinsolver – Simulator for Biochemical and Gene Regulatory Networks
- GENOME 0.2 – Rapid Coalescent-based Whole Genome Simulator
- MAmodel 20060511 – Microarray Simulator
- CellLine – Stochastic Cell Lineage Simulator
- SGN Sim – Stochastic Genetic Networks Simulator
- SIMCEP 1.0 – Cell Image Simulator
- Ileum 3.0 – Isolated Guinea-Pig Ileum Simulator
- ReadSim 0.12 – Simulator for Sanger and 454 Sequencing
- Metasim 0.9.5 – Sequencing Simulator for Genomes and Metagenomes
- Ilya – Reaction-Diffusion Simulator
- BacSim – Simulator of Bacterial Growth
- Evolver – Whole-genome Sequence Evolution Simulator
- NFsim – Biochemical Reaction Simulator
- BCT 4.4 – Bacterial Chemotaxis Modelling & Simulator
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