
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 12taxon 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 frontend for the TreePuzzle 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 webaccess...

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 treelevel and oneloop diagrams in the Standard Model ... more efﬁcient and a userfriendly topology editor was added. The current version 3 features...

nanoflann
 Referenced in 10 articles
[sw22685]
 library for building KDTrees of datasets with different topologies: R2, R3 (point clouds...

TDBS
 Referenced in 1 article
[sw02822]
 specifically for the case of clustertree topologies. In fact, the current IEEE 802.15.4/ZigBee ... they support multihop networking in mesh topologies, but with no synchronization. Even though both ... mention the possible use of clustertree topologies, which combine multihop and synchronization features ... regarding the use of the clustertree 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 wellsupported clades, distribution of tMRCA ... topological uncertainty. Thus, DensiTree provides a quick method for qualitative analysis of tree sets. AVAILABILITY...