• RAxML

  • Referenced in 44 articles [sw07716]
  • infer a 10.000-taxon phylogenetic tree containing representative organisms from the three domains: Eukarya, Bacteria...
  • XPath

  • Referenced in 375 articles [sw15780]
  • Second Edition)]. The data model provides a tree representation of XML documents as well ... strings, and booleans, and sequences that may contain both references to nodes ... addressing of the nodes in an XML tree. XPath 2.0 is a superset of [XPath...
  • Dendroscope

  • Referenced in 12 articles [sw21230]
  • they are restricted to small trees containing only tens of thousands of taxa. Moreover, many ... interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations ... optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides...
  • Thaw

  • Referenced in 14 articles [sw01150]
  • convex polyhedron is a tree containing a line segment beginning at every vertex ... smooth surface is also a tree, but of finite length. We introduce a method...
  • GCMs

  • Referenced in 9 articles [sw04944]
  • file describes the structure of the tree and contains rudimentary instructions ... CHANGES file describes recent changes. The entire tree is also available as zip archive...
  • VineCopula

  • Referenced in 40 articles [sw08160]
  • contains tools for bivariate exploratory data analysis, bivariate copula selection and (vine) tree construction. Models...
  • hlib

  • Referenced in 75 articles [sw04080]
  • lower-level algebraic operations. The library contains functions for H- and H2-matrix arithmetics ... support routines for the creation of cluster trees, visualization and numerical quadrature. This...
  • SiRiUS

  • Referenced in 10 articles [sw22498]
  • supported by SiRiUS using hash tree constructions. SiRiUS contains a novel method of performing file...
  • TOPD/FMTS

  • Referenced in 6 articles [sw19992]
  • Single) program allows the comparison of trees that contain both orthologs and paralogs. Each option ... null hypothesis that the similarity between two trees is not better than chance expectation. Availability...
  • SuperFine

  • Referenced in 3 articles [sw29605]
  • estimation. Many research groups are estimating trees containing anywhere from a few thousands to hundreds ... estimation of a Tree of Life, containing perhaps as many as several million leaves. These ... approach to estimate a large species tree is to use phylogenetic estimation methods (such...
  • Stern-Brocot Tree

  • Referenced in 3 articles [sw28560]
  • Stern-Brocot tree contains all rational numbers exactly once and in their lowest terms ... formalise the Stern-Brocot tree as a coinductive tree using recursive and iterative specifications, which ... contains all the numbers as stated. Following Hinze, we prove that the Stern-Brocot tree...
  • FAMOCUTN

  • Referenced in 3 articles [sw25847]
  • with cutset evaluation for large fault trees containing many replicated gates and events. The usual ... method for multi-level representation of fault trees with replicated gates. This method finds...
  • SYMORO+

  • Referenced in 7 articles [sw29890]
  • robots can be serial, tree structure or containing closed loops. The package runs...
  • S-Cluster++

  • Referenced in 2 articles [sw29662]
  • fast program for solving the cluster containment problem for phylogenetic networks. Motivation: Comparative genomic studies ... phylogenetic networks are the tree and cluster containment problems. The former asks how to decide ... cluster in some tree displayed in a phylogenetic network. The cluster containment problem ... recombination network. Both the tree containment and CCP are NP-complete. Although...
  • ViennaRNA

  • Referenced in 23 articles [sw10504]
  • package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro...
  • SplitsTree

  • Referenced in 32 articles [sw12234]
  • evolutionary data. MOTIVATION: Real evolutionary data often contain a number of different and sometimes conflicting ... always clearly support a unique tree. To address this problem, Bandelt and Dress (Adv. Math...
  • rpartOrdinal

  • Referenced in 6 articles [sw11730]
  • package rpartOrdinal: Ordinal classification tree functions. This package contains functions that can be called...
  • rpartScore

  • Referenced in 6 articles [sw14366]
  • package rpartScore: Classification trees for ordinal responses. This package contains functions that allow to build...
  • bartCause

  • Referenced in 2 articles [sw40926]
  • Causal Inference using Bayesian Additive Regression Trees. Contains a variety of methods to generate typical ... causal inference estimates using Bayesian Additive Regression Trees (BART) as the underlying regression model (Hill...
  • KRIPKE

  • Referenced in 8 articles [sw01162]
  • proof-search which will contain as a sub-tree a proof of A if there...