• PhylogeneticTrees

  • Referenced in 4 articles [sw41769]
  • allows users to compute phylogenetic invariants for group-based tree models. We provide some background...
  • HyDe

  • Referenced in 2 articles [sw29663]
  • branches of the gene trees. For certain models, site patterns are predicted to occur ... producing a set of functions called phylogenetic invariants. In this article, we introduce HyDe ... detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written...
  • ProtTest 3

  • Referenced in 4 articles [sw23032]
  • maximum likelihood (ML) estimation of phylogenetic trees and model parameters. The current version of ProtTest ... different models when we consider rate variation among sites (+I: invariable sites; +G: gamma-distributed...
  • GARLI

  • Referenced in 1 article [sw29598]
  • GARLI performs heuristic phylogenetic searches under the General Time Reversible (GTR) model of nucleotide substitution ... distributed rate heterogeneity and a proportion of invariant sites. The implementation of this model...
  • ATLAS

  • Referenced in 199 articles [sw00056]
  • This paper describes the Automatically Tuned Linear Algebra...
  • Cuba

  • Referenced in 77 articles [sw00173]
  • Cuba -- a library for multidimensional numerical integration. The...
  • GAP

  • Referenced in 3189 articles [sw00320]
  • GAP is a system for computational discrete algebra...
  • Macaulay2

  • Referenced in 1923 articles [sw00537]
  • Macaulay2 is a software system devoted to supporting...
  • Magma

  • Referenced in 3315 articles [sw00540]
  • Computer algebra system (CAS). Magma is a large...
  • Maple

  • Referenced in 5373 articles [sw00545]
  • The result of over 30 years of cutting...
  • Mathematica

  • Referenced in 6355 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 13544 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • MiniSat

  • Referenced in 566 articles [sw00577]
  • An extensible SAT-solver. MiniSat is a minimalistic...
  • Normaliz

  • Referenced in 172 articles [sw00630]
  • Normaliz is a tool for computations in affine...
  • polymake

  • Referenced in 316 articles [sw00724]
  • polymake is open source software for research in...
  • R

  • Referenced in 9969 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 1994 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • SINGULAR

  • Referenced in 1508 articles [sw00866]
  • SINGULAR is a Computer Algebra system (CAS) for...
  • TSPLIB

  • Referenced in 698 articles [sw00983]
  • TSPLIB is a library of sample instances for...