List of Software

This article was originally written by Daniel Spitz for the STRUCTURES Wiki (captured October 2025).

In recent years, a whole landscape of software emerged that deals with computational topology tasks in different fashions. On this page, we provide starting points for the selection of software suited for the problem of interest.

Packages described here include the following:

  • CGAL (https://www.cgal.org/)
  • JavaPlex (https://github.com/appliedtopology/javaplex), Tutorial
  • GUDHI (http://gudhi.gforge.inria.fr/), Tutorial
  • Ripser (https://github.com/Ripser)
  • PHAT (https://github.com/blazs/phat)
  • Dionysus (http://www.mrzv.org/software/dionysus)
  • R-Package TDA (https://cran.r-project.org/web/packages/TDA/index.html)
  • Perseus (http://www.sas.upenn.edu/~vnanda/perseus/index.html)
  • Rivet (http://rivet.online/)

This collection has been created without any claim of comprehensiveness. Whoever is aware of interesting topological data analysis software packages not listed here may contact the authors by mail at structures-hiwi@mathi.uni-heidelberg.de.

Overview

The following table summarizes information from Otter et al and Wikipedia. Nomenclature within the following table follows Otter et al . Software | CGAL | JavaPlex | GUDHI | Ripser | PHAT | Dionysus | R-Package TDA | Perseus | Rivet Language | C++ | Java, Matlab | C++ | C++ | C++, Python bindings | C++, Python bindings | R | C++ | stand-alone Filtrations computed | alpha | VR, W, W_v | VR, alpha, W, lower star of cubical complex | VR | - | VR, alpha, Čech | VR, alpha, sublevels of function on grid | VR, lower star of cubical complex | VR Persistent homology computation | no | yes | yes | yes | yes | yes | yes | yes | yes Homology | - | simplicial, cellular | simplicial | simplicial | simplicial, cubical | simplicial | simplicial | simplicial, cubical | simplicial Coefficient field | - | [math]\mathbb{Q}[/math], [math]\mathbb{F}_p[/math] | [math]\mathbb{F}_p[/math] | [math]\mathbb{F}_p[/math] | [math]\mathbb{F}_2[/math] | [math]\mathbb{F}_2[/math] (standard, zigzag), [math]\mathbb{F}_p[/math] (dual) | [math]\mathbb{F}_2[/math]? | [math]\mathbb{F}_2[/math] | [math]\mathbb{F}_2[/math]? Remarks | Provides a lot of versatile geometry algorithms | Routines for two-dimensional persistence computations

Details

CGAL

The basic design of CGAL is described in Fabri et al 2000.

The software’s webpage can be found here: https://www.cgal.org/.

JavaPlex

The basic design of JavaPlex is described in Adams et al 2014.

We provide an introductory tutorial to Javaplex on a different page.

The software’s webpage can be found here: https://www.cgal.org/.

GUDHI

The basic design of GUDHI is described in Maria et al 2014.

We provide an introductory tutorial to using GUDHI on a different page.

The software’s webpage including tons of useful example codes can be found here: http://gudhi.gforge.inria.fr/.

Ripser

The software’s webpage can be found here: https://github.com/Ripser.

PHAT

The basic design of the Persistent Homology Algorithms Toolbox (PHAT) is described in Bauer et al 2017.

The software’s webpage can be found here: https://github.com/blazs/phat.

Dionysus

The software’s webpage can be found here: http://www.mrzv.org/software/dionysus.

R-Package TDA

The Package TDA provides an R interface for the algorithms of the C++ libraries GUDHI, Dionysus and PHAT.

For an extensive reference manual and further information the reader may consult https://cran.r-project.org/web/packages/TDA/index.html.

Perseus

The efficient Morse-theoretic algorithm to compute persistent homology implemented in Perseus has been descibed first in Mischaikow and Nanda 2013.

For details on the software we refer to http://www.sas.upenn.edu/~vnanda/perseus/index.html.

Rivet

The software Rivet is described in . The software’s webpage can be found here: http://rivet.online/.