The "SimBa" software can compute persistence of input data embedded in (high dimensional) Euclidean space and in general metric spaces. It approximates the Rips filtration efficiently with theoretical guarantee.
The "SimPers" software can be used in the following case: Given a sequence of simplicial maps f1, f2,...fn between an initial simplicial complex K and a resulting simplicial complex L, the Simpers uses the annotation-based method developed in the paper below to compute the persistence of the sequence of simplicial maps, that is the ranks of image H(K)--f1--f2--...--fn--> H(L) in all dimensions.
The "PersistenceDistortion" software is for computing Discrete Persistence Distortion between metric graphs. Given two metric graphs G1 and G2, the "PersistenceDistortion" computes the persistence distortion distance between them, which measures the metric distortion between two graphs.
Graph Induced Complex
The "Graph induced complex" software is for topological inference and surface reconstruction from point data. It enjoys the the advantages of both Vietoris-Rips and witness complexes. It only needs a graph connecting the original sample points from which it builds a complex on the subsample thus taming the size considerably.
The "ShortLoop" software can compute a set of non-trivial loops from point cloud data/simplicial complexes that represent a shortest homology basis. The simplicial complex need not be a surface and thus the software can handle very general input of triangulated domains with non-manifold artifacts. If the input is a point cloud data sampled from a smooth manifold, the loops will approximate a true shortest homology basis of the manifold.
A software package (developed by [J. Eldridge]) for a terrain metaphor platform for general scalar trees, with a callback system for general data analysis applications. The algorithm behind the software is based on our earlier work [Harvey and Wang, CFG2010]. Our software Ayla below is a collaborative and integrative framework targeted at molecular simulation data sets, while Denali aims to serve as a generic framework for general data.
The Morse-based map reconstruction software developed by [Suyi Wang]).