• SnapPea

  • Referenced in 163 articles [sw06873]
  • listed: volume, Chern-Simons invariant (if orientable), homology, symmetry or isometry group, shortest geodesic, chirality...
  • CAPD

  • Referenced in 77 articles [sw07620]
  • which are mainly designed to computation of homology of sets and maps and nonrigorous...
  • Gudhi

  • Referenced in 38 articles [sw08777]
  • Gudhi Library: Simplicial Complexes and Persistent Homology. We present the main algorithmic and design choices ... simplicial complexes and the computation of persistent homology in the Gudhi library. The Gudhi library ... points, and then compute the persistent homology of these complexes. The simplicial complex and persistent ... homology packages in Gudhi provide all software components for this approach. Specifically, simplicial complexes...
  • CHomP

  • Referenced in 51 articles [sw09358]
  • CHomP, Computational homology project. Much of the fascination and challenge of studying nonlinear systems arises ... nonlinear spaces and functions, within which homology is perhaps the most computable subset. In particular...
  • PatternHunter

  • Referenced in 36 articles [sw20963]
  • PatternHunter: faster and more sensitive homology search. MOTIVATION: Genomics and proteomics studies routinely depend ... homology searches based on the strategy of finding short seed matches which are then extended ... data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity ... down computation. RESULTS: We present a new homology search algorithm ’PatternHunter’ that uses a novel...
  • Kenzo

  • Referenced in 65 articles [sw04861]
  • ideas of the second author about Effective Homology, mainly around the Serre and Eilenberg-Moore...
  • PersistenceImages

  • Referenced in 35 articles [sw41418]
  • Images: A Stable Vector Representation of Persistent Homology. Many datasets can be viewed ... knowledge discovery. One such tool is persistent homology, which provides a multiscale description ... homological features within a dataset. A useful representation of this homological information is a persistence...
  • Homology

  • Referenced in 30 articles [sw04871]
  • Computing simplicial homology based on efficient Smith normal form algorithms Geometric properties of topological spaces ... methods for the computer calculation of the homology of finite simplicial complexes and its applications ... calculation of homology with integer coefficients of a simplicial complex reduces to the calculation ... alternative approaches to the calculation of simplicial homology. In the last section they present motivating...
  • HAP

  • Referenced in 39 articles [sw04870]
  • homological algebra library for use with the GAP computer algebra system, and is still under ... Recent additions include some functions for computing homology of crossed modules and simplicial groups...
  • javaPlex

  • Referenced in 39 articles [sw08779]
  • Stanford-based Plex family of persistent homology and cohomology software packages. Written in Java ... platform support absolute and relative persistence (co)homology, as well as hom-complexes of simplicial...
  • PHAT

  • Referenced in 39 articles [sw08780]
  • PHAT - Persistent Homology Algorithms Toolbox. PHAT is a C++ library for the computation of persistent ... homology. This task is usually split into two major tasks: (1) building a boundary matrix...
  • Perseus

  • Referenced in 29 articles [sw08778]
  • Discrete Morse Homology and the Perseus Software Project. At its core, the computation of homology ... linear time while preserving all the underlying homological information. In this talk, we outline ... methods in order to efficiently compute persistent homology of various types of filtered complexes...
  • BLAT

  • Referenced in 36 articles [sw16891]
  • regions in the genome likely to be homologous to the query sequence. It performs ... alignment between homologous regions. It stitches together these aligned regions (often exons) into larger alignments...
  • iSNO-PseAAC

  • Referenced in 39 articles [sw22446]
  • sites. To reduce the homology bias, none of these sites were derived from the proteins...
  • MEGA

  • Referenced in 35 articles [sw09078]
  • desktop application designed for comparative analysis of homologous gene sequences either from multigene families...
  • MODELLER

  • Referenced in 34 articles [sw27731]
  • Protein Structure Modeling. MODELLER is used for homology or comparative modeling of protein three-dimensional...
  • Euk-PLoc

  • Referenced in 24 articles [sw22420]
  • unknown query proteins do not have significant homology to proteins of known subcellular locations ... body, and (18) vacuole. To avoid the homology bias, none of the proteins included...
  • Hum-PLoc

  • Referenced in 24 articles [sw26863]
  • unknown query proteins do not have significant homology to proteins of known subcellular locations ... membrane. To get rid of redundancy and homology bias, none of the proteins investigated here...
  • homalg

  • Referenced in 30 articles [sw00411]
  • homalg: a meta-package for homological algebra. The central notion of this work is that...