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Compare scientific models products for capabilities, deployment, pricing, and enterprise readiness. Ranked using verified practitioner feedback, product research, and enterprise trust signals.
| Company | Description | Matching products |
|---|---|---|
| BEAST | A cross-platform program for Bayesian analysis of molecular sequences using MCMC, oriented toward rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. Serves as a framework for reconstructing phylogenies and testing evolutionary hypotheses without conditioning on a single tree topology. | |
| BEAST 2 | Cross-platform program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models and serves as a framework for testing evolutionary hypotheses without conditioning on a single tree topology. Uses Markov chain Monte Carlo (MCMC) to average over tree space. |
| BECKER 3D | Engineering service provider offering 3D simulation software (ThreeParticle/CAE), trainings, technical support, development, and consulting engineering. |
| BQCD | Berlin quantum chromodynamics program — a Hybrid Monte-Carlo program that simulates lattice QCD with dynamical Wilson fermions, used for nuclear and high energy physics calculations. |
| Beicip-Franlab | International energy consultancy and software solutions provider with almost 60 years of activity, offering services from exploration to field development and production across subsurface energy domains. |
| Bonito | An open source research basecaller for Oxford Nanopore reads, developed and maintained by Oxford Nanopore Technologies (nanoporetech). |
| CADISHI | CADISHI (CAlculation of DIStance HIstograms) is a software package that enables scientists to compute Euclidean distance histograms efficiently from sets of objects with 3D Cartesian coordinates, e.g., atoms in molecular dynamics datasets or galaxies in astrophysical contexts. |
| CHARMM | Chemistry at HARvard Macromolecular Mechanics. A molecular simulation program with broad application to many-particle systems, actively maintained by a large group of developers led by Martin Karplus. |
| COSMO | Consortium formed in October 1998 to develop, improve, and maintain a non-hydrostatic limited-area atmospheric model for operational and research applications by member organizations. |
| CP2K Open Source Molecular Dynamics | Open source quantum chemistry and solid state physics software package for atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. |
| CPFD Software | CPFD Software advances multiphase simulation and technology for fluid-particle systems. |
| CUDASW++ | Open-source bioinformatics software for Smith-Waterman protein database searches accelerated on NVIDIA GPUs. |
| CUSHAW | Next-generation sequencing read alignment software package based on multi-core and many-core computing, developed by Yongchao Liu and hosted on SourceForge. |
| Cadence Design Systems, Inc. | Company behind the Fidelity CFD software platform, providing an end-to-end CFD solution for multidisciplinary design and optimization. |
| Cellpose | A generalist algorithm for cellular segmentation with human-in-the-loop capabilities, developed under the GitHub organization MouseLand. |
| ChaNGa | Open-source astrophysics code (Charm N-body GrAvity solver) for collisionless N-body simulations, hosted under the N-BodyShop organization on GitHub. Described as the UIUC/PPL version of ChaNGa. |
| Clair3 | Clair3 is a germline small variant caller for long reads developed by HKU-BAL. It combines pileup calling and full-alignment approaches for high-performance long-read variant calling. |
| Classiq | Your guide to high-level quantum programming. Code faster, implement better, run anywhere. |
| Colvars | Collective variables library for molecular simulation and analysis programs. A software library providing a high-performance implementation of sampling algorithms defined on a reduced space of continuously differentiable functions (collective variables). |
| Computational Crystallography Toolbox | Open source component of the Phenix project to advance automation of macromolecular structure determination. Useful for small-molecule crystallography and general scientific applications. |
| CryoSPARC | Structura Biotechnology Inc. develops and supports CryoSPARC, software for cryo-electron microscopy (cryo-EM) data processing used in drug discovery and research. Based in Toronto, Canada. | CryoSPARC 1 more |
| CuCLARK | CuCLARK is a metagenomic classifier for CUDA-enabled GPUs, based on CLARK. Authored by Robin Kobus at the Institute of Computer Science, JGU Mainz, Germany. |
| Cytocast | Techbio startup using AI-powered predictive modeling to evaluate drug side effects of chemical compounds. |
| DFT-FE | Massively parallel real-space C++ code for first-principles materials modelling using Kohn-Sham density functional theory (DFT), based on adaptive finite-element discretization. It handles pseudopotential and all-electron calculations with periodic, non-periodic, and semi-periodic boundary conditions. |
| DHI | Develops and operates the MIKE Powered by DHI water modelling software suite and digital solutions for analysing, modelling, and simulating diverse water environments. |
| Dassault Systèmes | Dassault Systèmes' 3DEXPERIENCE on the Cloud platform — a single collaborative environment connecting people, ideas, data and solutions (SaaS, PaaS, IaaS). |
| DeePMD-kit | An open-source package written in Python/C++, designed to minimize the effort required to build deep learning-based models of interatomic potential energy and force fields and to perform molecular dynamics. |
| Deep Genomics | AI-driven genetic medicines platform company that collaborates across disciplines to solve molecular design and target biology problems in drug discovery. |
| DeepChain | Industry-leading biology AI solutions for life sciences R&D, built on InstaDeep's AI research. |
| DeepCombi | A Python framework for the analysis of GWAS data with special focus on explainable artificial intelligence. Developed by Alexandre Rozier and Bettina Mieth. |
| DeepFlow | Open-source research software project for reconstructing cell cycle and disease progression using deep learning from flow cytometry data. Hosted under the theislab GitHub organization. |
| DeepMicrobes | Deep learning-based computational framework for taxonomic classification of metagenomic data, allowing researchers to bypass the limitation of a well-curated taxonomic tree for newly discovered species. |
| DeepSim | AI-driven multi-scale physics simulation platform enabling 1000X faster simulations with simultaneous nano-to-macro scale resolution. |
| DeepVariant | DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. |
| Dorado | High-performance, easy-to-use, open source analysis engine for Oxford Nanopore reads. |
| Dynamo | Dynamo is a software environment for subtomogram averaging of cryo-EM data. The wiki guides users from tomograms through catalogues, particle picking, alignment, and classification projects across different computing environments. |
| EDDY | EDDY (Evaluation of Differential DependencY) is an algorithm developed by the Biocomputing Lab at TGen and maintained at the CRI Center for Computational Systems Biology at Prairie View A&M University. |
| ELPA | ELPA (Eigenvalue soLvers for Petaflop Applications) provides highly efficient and scalable direct eigensolvers for symmetric matrices of all sizes, associated with the Max Planck Computing and Data Facility. |
| EMAN2 | A broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes, supporting single particle reconstruction, single particle cryo-ET, helical reconstruction, 2-D crystallography, and whole-cell tomography. |
| ESPResSo | Highly versatile open-source software package for performing and analyzing scientific Molecular Dynamics and many-particle simulations of coarse-grained atomistic or bead-spring models used in soft matter research in physics, chemistry, and molecular biology. |
| ESS Engineering Software Steyr GmbH | Engineering software company and developer of alsim Paint Shop, a paint shop simulation toolbox for automotive processes. |
| ElPiGraph-python | Open-source Python package providing a Python implementation of the ElPiGraph algorithm with CPU and GPU support. |
| FIFTY2 Technology GmbH | FIFTY2 Technology is the developer of PreonLab, a leading-edge particle-based CFD simulation software focusing on rapid prototyping and high-performance physics. |
| FlexSim | 3D simulation modeling software company offering tools to model, analyze, and improve systems across manufacturing, healthcare, supply chain, warehousing, logistics, aerospace, mining, and beyond. |
| FlexTerm | Digital twin, simulation, and emulation software for port and logistics operators, enabling analysis, design, optimization, and testing of facility systems before production deployment. |
| FloodWaive | AI-powered flood prediction and risk analysis solutions for public and private stakeholders. |
| Folding@home | A distributed computing project for biomedical research that turns volunteers' idle computer power into a global supercomputer. Led by Dr. Greg Bowman and the Folding@home Consortium, a network of academic labs across the globe, running since October 2000. |
| GAMER | GPU-accelerated Adaptive-MEsh-Refinement code for astrophysical applications, solving hydrodynamics with self-gravity. |
| GHOSTZ-GPU | An open-source GPU-accelerated sequence homology search tool using database subsequence clustering, hosted in the akiyamalab repository on GitHub. |
| GNS | GNS mbH (Gesellschaft für numerische Simulation mbH) develops CAE software, compute models, and process automation for structural analysis, crash & safety, NVH, and sheet metal forming. |