PH-roadmap
Project founder:
Nina Otter (For contact information, see here.)
Description
This project was created to host data sets and scripts used in the paper [1] and the accompanying supplementary information.
Software for PH
In the following you can find all libraries to compute PH that I know of. If you know a package that is not listed here, please contact me. I was inspired to write this list by Felsenstein's comprehensive list of phylogeny programs.| Brief introduction | By complexes | By language | Statistical tools |
Brief Introduction
If you are new to the computation of persistent homology a good idea is to start with javaPlex, which is the new library of the Plex family:
After that you could try out Perseus, which implements Morse theoretic reductions to reduce the size of the complex:
If you are familiar with R you might want to try out these two libraries:
-
pHom
- TDA (See here for the accompanying tutorial.) This library implements many tools for the statistical interpretation of the computation of PH.
....and if you are familiar with GAP this one:
The following is a powerful toolbox of algorithms for the computation of barcodes from the boundary matrix (the first package to implement parallel computation in a shared setting):
....if you do not want to compute the boundary matrix yourself, you can use its spin-off library (which implements algorithms for parallel computations in a distributed setting):
Another powerful software is this:
This is the only software to implement, among other things, the computation of PH with the Čech complex, and vineyards:
...while the following library implements, among other things, a parallel computation of homology based on the Mayer-Vietoris principle and the computation of PH over finite fields:
The following is a module for the Kenzo library which implements computation of PH in a more general setting, i.e. with integer coefficients and for infinite spaces (provided their homology is effective):
- Kenzo module for PH (see the companion preprint for instructions)
Finally some more libraries:
....to do statistics on persistence diagrams:
....for simplicial maps:
....to compute the weight rank clique filtration for networks:
....and its older version:
....for fast computation of PH with alpha complexes in 1-D: