• SNV-PPILP

  • Referenced in 2 articles [sw23968]
  • calling for tumor data using perfect phylogenies and ILP. MOTIVATION: Recent studies sequenced tumor samples ... multiple samples assumed to form a phylogeny. We tested SNV-PPILP on simulated data, with ... read coverage and violations of the perfect phylogeny assumption. We always match or improve...
  • HTreeQA

  • Referenced in 1 article [sw20045]
  • HTreeQA: Using semi-perfect phylogeny trees in quantitative trait loci study on genotype data. With ... recently has attracted significant research attention. Local phylogeny-based methods have been demonstrated ... HTreeQA, that uses a tristate semi-perfect phylogeny tree to approximate the perfect phylogeny used ... existing methods. The semi-perfect phylogeny trees are used as high-level markers for association...
  • FlipCut

  • Referenced in 2 articles [sw08374]
  • resulting matrix admits a directed perfect phylogeny. We then extend our approach by using edge...
  • TreeQA

  • Referenced in 1 article [sw20041]
  • genome wide association mapping using local perfect phylogeny trees. The goal of genome wide association ... mapping algorithm. TreeQA utilizes local perfect phylogenies constructed in genomic regions exhibiting no evidence...
  • SPRUCE

  • Referenced in 1 article [sw34279]
  • algorithm that infers a multi-state perfect phylogeny describing the evolutionary history of the somatic...
  • SPhyR

  • Referenced in 1 article [sw34136]
  • Phylogeny Reconstruction (SPhyR), a method for tumor phylogeny estimation from single-cell sequencing data ... connection to the cladistic multi-state perfect phylogeny problem. SPhyR outperforms existing methods on simulated...
  • GAP

  • Referenced in 2735 articles [sw00320]
  • GAP is a system for computational discrete algebra...
  • Mathematica

  • Referenced in 5756 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 11649 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • TSPLIB

  • Referenced in 657 articles [sw00983]
  • TSPLIB is a library of sample instances for...
  • fda (R)

  • Referenced in 1217 articles [sw04511]
  • fda: Functional Data Analysis , These functions were developed...
  • HAPLO

  • Referenced in 23 articles [sw04580]
  • HAPLO: A Program Using the EM Algorithm to...
  • OEIS

  • Referenced in 3220 articles [sw07248]
  • The On-Line Encyclopedia of Integer Sequence. The...
  • RAxML

  • Referenced in 33 articles [sw07716]
  • Parallel inference of a 10.000-taxon phylogeny with...
  • PAUP*

  • Referenced in 51 articles [sw07834]
  • PAUP*: phylogenetic analysis under parsimony. PAUP* version 4.0...
  • EPoS

  • Referenced in 4 articles [sw08375]
  • EPoS: a modular software framework for phylogenetic analysis...
  • PhySIC

  • Referenced in 8 articles [sw08376]
  • PhySIC: A Veto Supertree Method with Desirable Properties...
  • bootstrap

  • Referenced in 997 articles [sw19105]
  • R package bootstrap. bootstrap: Functions for the Book...
  • GitHub

  • Referenced in 1337 articles [sw23170]
  • GitHub (originally known as Logical Awesome LLC)[3...
  • SuperTriplets

  • Referenced in 3 articles [sw29604]
  • SuperTriplets: a triplet-based supertree approach to phylogenomics...