modeling
- ModFit LT 4.0 – Flow Cytometry Modeling
- DLCoal 1.0 – Modeling Gene Duplications, Losses, and Coalescence
- YASARA 13.4.21 – Molecular Graphics, Modeling & Simulation program
- ProDy 1.4.2 – Python package for Analysis and Modeling of Protein Structural Dynamics
- PottersWheel 3.0 – MatLab Toolbox of Mathematical Modeling of Dynamical Systems
- VCell 5.1 – Environment for Modeling & Simulation of Cell Biology
- GeneNet 1.2.6 – Modeling and Inferring Gene Networks
- ProbRNA 1.0 – Modeling RNA Structure Probing data
- mseq 1.2 – Modeling non-uniformity in Short-read Rates in RNA-Seq data
- BRAGI 20091106 – A Protein Visualization and Modeling Program
- SurreyFBA 1.32 – Constraint-based modeling of Genome-scale Metabolic Reaction Networks
- MODELLER 9.11 – Comparative Protein Structure Modeling
- ProtMod – Protein Modeling Server
- BioNet Reasoning – Modeling Biological Systems
- RLooM – RNA Loop Modeling
- LigandScout 3.1b – Pharmacophore 3D Modeling
- BiPad – Web Server for Modeling Bipartite Sequence Elements
- PyRy3D 1.0.0 – Modeling of large Macromolecular Complexes
- AMMP 2.0 – Molecular Mechanics, Dynamics and Modeling program
- IMOD 4.5.7 – Tomographic 3D Reconstruction & Modeling
- COBRA Toolbox 2.0.5 – MATLAB Scripts for Constraint-based Modeling of Metabolic Networks
- RepeatModeler 1.0.5 – de-novo Repeat Family Identification and Modeling package
- RAPTOR 4.5 – Protein Structure Modeling
- ModeRNA 1.7.1 – Comparative RNA 3D Modeling
- SloppyCell – system for Modeling Biochemical Reaction Networks
- Bodil 0.8.1 – Biomolecular Visualization and Modeling
- REvolver 1.0 – Modeling Sequence Evolution under Domain Constraints
- PrISM – Protein Informatics System for Modeling
- Jackal 1.5 – Protein Structure Modeling Package
- RD – Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
- MetaReg – Graphical Interface for Modeling and Evaluation of Biological Systems
- PNK 2e – Modeling and Simulation of Biological Processes
- JigCell 7.1.0 – Modeling and Simulation software
- MotifBooster – Transcriptional Regulatory Motif Modeling and Discovery
- RW 1.0 – Protein Structure Modeling and Structure Decoy Recognition
- MolIDE 1.7 – Protein 3D Homology Modeling
- TASSER-Lite 1.0 – Protein Structure Modeling tool
- Cellware 3.0.1 – Modeling & Simulation Tool for Modeling Cellular Transactions
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