• SplitsTree

  • Referenced in 32 articles [sw12234]
  • number of different and sometimes conflicting phylogenetic signals, and thus do not always clearly support...
  • PhySIC

  • Referenced in 8 articles [sw08376]
  • Moreover, we introduce the PhySIC method (PHYlogenetic Signal with Induction and non-Contradiction...
  • adephylo

  • Referenced in 3 articles [sw08303]
  • adephylo: new tools for investigating the phylogenetic signal in biological traits. adephylo is a package ... removing the effects of phylogenetic signal in the analysis of biological traits. However, recent approaches ... gathered from the study of the phylogenetic signal. In particular, close examination of phylogenetic structures ... biological traits. adephylo implements tests of phylogenetic signal, phylogenetic distances and proximities, and novel methods...
  • Phylocom

  • Referenced in 3 articles [sw27224]
  • Within the same framework, it measures phylogenetic signal and correlated evolution for species traits ... range of utility functions allow community and phylogenetic data manipulation, tree and trait generation...
  • Noisy

  • Referenced in 5 articles [sw21022]
  • leads to a patchwork pattern of (i) phylogenetically informative and (ii) effectively randomized regions ... errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. RESULTS: We present here...
  • RevTrans

  • Referenced in 2 articles [sw37903]
  • contains four different bases, means that the ‘signal-to-noise ratio’ in protein sequence alignments ... synonymous ones, this means that the phylogenetic signal disappears much more rapidly from DNA sequences ... useful when constructing multiple DNA alignments for phylogenetic analysis. RevTrans also accepts user-provided protein...
  • PhyloScan

  • Referenced in 3 articles [sw34212]
  • statistic over the phylogenetic tree to allow nodes to borrow signal strength from their parents...
  • PSICOV

  • Referenced in 7 articles [sw17010]
  • often inaccurate because the true covariation signal in the MSA is often masked by biases ... from many ancillary indirect-coupling or phylogenetic effects. Here we present a novel method, PSICOV...
  • Statalign

  • Referenced in 5 articles [sw16609]
  • multiple alignment and consider only substitutions as phylogenetically informative mutations, though alignments and phylogenies should ... insertions and deletions also carry informative signals. Methods addressing these issues have been developed only...
  • trimAl

  • Referenced in 3 articles [sw24603]
  • which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone ... each specific alignment so that the signal-to-noise ratio is optimized. AVAILABILITY: trimAl...
  • FunCoup

  • Referenced in 1 article [sw27475]
  • classes of couplings: participation in the same signaling cascade, participation in the same metabolic process ... evidences and a novel method to incorporate phylogenetic profile similarity. Several datasets have been updated...
  • 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...
  • 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...
  • PHCpack

  • Referenced in 236 articles [sw00705]
  • Algorithm 795: PHCpack: A general-purpose solver for...