What applied topology software options do I have?

This list undoubtably has unintentional omissions; please email Henry with updates to this list!

This list was originally created to accompany the tutorial https://github.com/henryadams/Charleston-TDA-ML for the NSF-CBMS Conference and Software Day on Topological Methods in Machine Learning and Artificial Intelligence.

• Mapper
  • Ayasdi.
  • giotto-tda is a library combining applied topology software with machine learning algorithms.
  • Mapper Interactive. A web-based framework for interactive analysis built upon the Mapper algorithm.
  • Scikit-TDA: Kepler Mapper. A flexible Python implementation of the Mapper algorithm.
  • TDA Mapper. An R package for using the Mapper algorithm.
  • Python Mapper. A python implementation of the Mapper algorithm.
• Persistent homology
  • CubicalRipser. Adaptation of Ripser (below) for cubical homology.
  • CHomP. Computational Homology Project. C++; Cubical homology.
  • DIPHA. A Distributed Persistent Homology Algorithm; C++.
  • Dionysus and Dionysus 2. Dionysus is a C++ library for computing persistent homology, equipped with python bindings. It provides implementations of the following algorithms: persistent (co)homology, vineyards, zigzag persistence, etc.
  • Eirene. Julia platform for computational topology.
  • Javaplex. Java and Matlab code, equipped with a tutorial with real-life data examples.
  • giotto-tda is a library combining applied topology software with machine learning algorithms.
  • GUDHI. The GUDHI library is a generic open source C++ library, with a Python interface, for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding. The library offers state-of-the-art data structures and algorithms to construct simplicial complexes and compute persistent homology. The library comes with data sets, demos, examples and test suites.
  • Perseus. A C++ software project for the rapid computation of persistent homology. Includes cubical and simplicial complexes.
  • PHAT. C++ code.
  • R-TDA. Tools for the statistical analysis of persistent homology and for density clustering. For that, this package provides an R interface for the efficient algorithms of the C++ libraries GUDHI, Dionysus, and PHAT. This package also implements methods for analyzing the statistical significance of persistent homology features.
  • Scikit-TDA. A home for Topological Data Analysis Python libraries intended for non-topologists. This project aims to provide a curated library of TDA Python tools that are widely usable and easily approachable. Contains Ripser.py as one subcomponent.
  • Ripser: efficient computation of Vietoris-Rips persistence barcodes. It is possible to run a beginner’s version of Ripser in your html browser, for which no installation is required.
  • Ripser++: a GPU-accelerated version of Ripser
  • Rivet. Extends the usual persistent homology pipeline for topological data analysis to the two-parameter setting.
  • SimBa. C++ software for approximating Rips filtration persistence via simplicial batch-collapse.
  • torch_topological. Topological machine learning with pytorch.
• Vectorizations of persistent homology
  • Persistence Landscape Toolbox. Code for computing persistence landscapes.
  • Persistence Images
    • Scikit-TDA: PerSim. A Python package for many tools used in analyzing Persistence Diagrams, including persistence images, bottleneck distance, sliced Wasserstein kernel, and then heat kernel.
    • CSU-TDA: PersistenceImages in Python. A Python package for persistence images.
    • CSU-TDA: PersistenceImages in Matlab. A Matlab package for persistence images.
    • PersistenceImage.jl. A Julia implementation of persistence images.
• Other
  • CliqueTop. Topological data analysis tools for cross correlation matrices and neuroscience.
  • FastZigzag. For zigzag persistence.
  • Flagser. Computing homology of directed flag complexes (based on Ripser).
  • Hera. Contains fast C++ code for distances between barcodes.
  • Time series analysis with TDA. Also contains python wrappers to various persistent homology software packages.
  • Topology ToolKit.
  • UMAP. Uniform Manifold Approximation and Projection.
• In September 2019 I gave a survey talk on the above software available at the time; see the video and my slides.
• Similar software lists are kept by Peter Bubenik, Chad Giusti, and this survey paper.

You may also be interested in this partial list of applied topology book options.

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