• BEAST

  • Referenced in 60 articles [sw12588]
  • hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo...
  • BIONJ

  • Referenced in 30 articles [sw08301]
  • have been performed with 12-taxon model trees to determine BIONJ’s efficiency. When ... vary among lineages,BIONJ clearly has better topological accuracy. In the latter case ... model trees and the conditions of evolution tested, the topological error reduction...
  • QNet

  • Referenced in 11 articles [sw19662]
  • input the set of all quartet tree topologies for a given data set, together with ... branch length for each topology. These branch lengths must be precomputed by the user. Included ... LengthWeighter is a front-end for the Tree-Puzzle software [3] for generating likelihood quartet...
  • PhyML

  • Referenced in 11 articles [sw10915]
  • search the space of phylogenetic tree topologies, going from very fast and efficient methods...
  • apTreeshape

  • Referenced in 9 articles [sw31620]
  • Treeshape. Simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion ... additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access...
  • iGLASS

  • Referenced in 4 articles [sw29611]
  • these methods provide consistent species tree topology estimates under a standard model, most either ... Roch, is consistent for the species tree topology, estimates branch lengths, and is computationally fast ... times, leading to biased estimates of species tree branch lengths. By assuming a multispecies coalescent ... consistent estimator of the species tree topology. Through simulations, we show that iGLASS can greatly...
  • TreeFix

  • Referenced in 6 articles [sw29607]
  • information to confidently support one gene tree topology over many competing alternatives. Here, we present ... framework for combining sequence data and species tree information, and we describe an implementation...
  • MAppleT

  • Referenced in 4 articles [sw14380]
  • capture event dynamics, especially when both tree topology and geometry are considered. The present project ... topology and geometry in a single simulation such that the architecture of an apple tree ... based on stochastic models to simulate plant topology and mechanistic model for the geometry ... geometric models representing the progression of tree form over time. To asses these models...
  • AWTY

  • Referenced in 4 articles [sw18698]
  • long enough, such that tree topologies are being sampled in proportion to their true posterior...
  • FeynArts

  • Referenced in 115 articles [sw06474]
  • Sepp Küblbeck which could produce tree-level and one-loop diagrams in the Standard Model ... more efficient and a user-friendly topology editor was added. The current version 3 features...
  • nanoflann

  • Referenced in 10 articles [sw22685]
  • library for building KD-Trees of datasets with different topologies: R2, R3 (point clouds...
  • TDBS

  • Referenced in 1 article [sw02822]
  • specifically for the case of cluster-tree topologies. In fact, the current IEEE 802.15.4/ZigBee ... they support multi-hop networking in mesh topologies, but with no synchronization. Even though both ... mention the possible use of cluster-tree topologies, which combine multi-hop and synchronization features ... regarding the use of the cluster-tree topology and proposing a synchronization mechanism based...
  • MulRF

  • Referenced in 3 articles [sw23051]
  • Weighted input gene trees for species tree search. Topological constraints on the inferred species tree...
  • STELLS2

  • Referenced in 2 articles [sw32301]
  • inference of species trees from gene tree topologies. STELLS is a program for finding...
  • PhyloBayes MPI

  • Referenced in 2 articles [sw23042]
  • partial Gibbs sampling update of the tree topology and the use of a truncated stick...
  • PRANC

  • Referenced in 1 article [sw40985]
  • computes the Probabilities of RANked gene tree topologies under the multispecies coalescent. A ranked gene ... sample of ranked or unranked gene tree topologies. It estimates the ML tree with estimated...
  • PAxML

  • Referenced in 1 article [sw06653]
  • calculating the likelihood value for each tree topology. It accounts for the greatest part ... maximum likelihood value for a given tree topology by using SEVs (Subtree Equality Vectors...
  • StarBEAST2

  • Referenced in 1 article [sw29665]
  • inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious ... more accurate inference of species tree topologies, divergence times, and substitution rates, we have developed ... species substitution rates, we introduce species tree relaxed clocks, and show that StarBEAST2...
  • Gudhi

  • Referenced in 43 articles [sw08777]
  • analysis, where one is interested in learning topological invariants of a shape, sampled ... simplicial complexes are implemented with a simplex tree data structure. The simplex tree ... persistent homology, and provides the same topological invariant represented by a persistence diagram. The persistent...
  • DensiTree

  • Referenced in 3 articles [sw23034]
  • where a lot of the trees agree in topology and branch lengths show ... impression of properties of the tree set such as well-supported clades, distribution of tMRCA ... topological uncertainty. Thus, DensiTree provides a quick method for qualitative analysis of tree sets. AVAILABILITY...