• Quartets MaxCut

  • Referenced in 7 articles [sw29616]
  • Hence, in order to construct the tree of life over a million and a half ... This problem lies at the root of many tree reconstruction methods and theoretical as well ... ours [29] for piecing together trees from rooted triplet trees. The recursion for unrooted quartets...
  • Root Balanced Tree

  • Referenced in 4 articles [sw28657]
  • Root-Balanced Tree. Andersson introduced general balanced trees, search trees based on the design principle ... general balanced trees, which we call root-balanced trees. Using a lightweight model of execution ... APLAS 2017 article Verified Root-Balanced Trees by the same author, which also presents experimental ... show competitiveness of root-balanced with AVL and red-black trees...
  • Notung

  • Referenced in 13 articles [sw08917]
  • vertebrate genomes. The use of evolutionary trees to analyze the history of gene duplication ... large scale analysis, using both rooted and unrooted trees. When tested on trees analyzed...
  • SackinMinimizer

  • Referenced in 5 articles [sw39018]
  • binary (search) trees, not for general rooted trees. Moreover, while the number of trees with...
  • Devmol

  • Referenced in 3 articles [sw00199]
  • expansions, namely for the species of “Rooted trees” and of “Husimi graphs”, weighted by their ... with two examples of applications, to rooted trees weighted by a leaf counter...
  • Tanglegrams

  • Referenced in 4 articles [sw21231]
  • Tanglegrams for rooted phylogenetic trees and networks. MOTIVATION: In systematic biology, one is often faced ... with the task of comparing different phylogenetic trees, in particular in multi-gene analysis ... tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines ... There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history...
  • NodePy

  • Referenced in 4 articles [sw12306]
  • conditions are generated using products on rooted trees (or other recursions) rather than being hard...
  • DupTree

  • Referenced in 4 articles [sw12376]
  • software program for inferring rooted species trees from collections of gene trees using the gene ... time of standard search heuristics for gene tree parsimony, and enables the first truly genome ... examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree...
  • treex

  • Referenced in 2 articles [sw32686]
  • Python library for manipulating rooted trees. The trees can be ordered or not, with ... package provides a data structure for rooted trees as well as the following main functionalities...
  • DESPOTA

  • Referenced in 3 articles [sw26834]
  • algorithm visits nodes from the tree root toward the leaves. At each node, it tests...
  • A435

  • Referenced in 2 articles [sw30551]
  • defined on the set of labeled rooted trees on n vertices. Going back to Neil ... A435): on the total heights in rooted labeled trees...
  • BEAST

  • Referenced in 48 articles [sw12588]
  • phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed ... evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte...
  • Triplet MaxCut

  • Referenced in 1 article [sw29615]
  • Triplet MaxCut: a new toolkit for rooted supertree. The rapid increase of molecular, as well ... information in the output tree. Triplets, rooted trees over three leaves, are the minimal piece ... such information when dealing with rooted trees. Due to its fundamental role in phylogenetics, extensive ... operations in rooted supertree, principally amalgamating rooted trees based on amalgamating rooted triplets. The utility...
  • iTOL

  • Referenced in 9 articles [sw33187]
  • phylogenetic trees. Trees can be interactively pruned and re-rooted. Various types of data such ... domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics...
  • SqFreeEVAL

  • Referenced in 11 articles [sw07421]
  • widely used for isolating the real roots of f in a given interval. In this ... compute the size of the subdivision tree for the SqFreeEVAL algorithm.The SqFreeEVAL algorithm ... tree for the SqFreeEVAL algorithm on the benchmark problem of isolating all real roots ... amortization technique of the standard Mahler-Davenport root bounds to interpret the integral in terms...
  • HybridNET

  • Referenced in 3 articles [sw14682]
  • another segment of sequences, a different phylogenetic tree can be obtained with high confidence ... have the following problem: given two rooted phylogenetic trees on a set of species that...
  • TREECON

  • Referenced in 1 article [sw33535]
  • these methods produce unrooted evolutionary trees, a program ROOT places a root on the tree ... only for nucleic acids, the modules TREE, ROOT and DRAW are applicable to any kind...
  • RANGER-DTL

  • Referenced in 1 article [sw34144]
  • reconciliation uncertainty including uncertain gene tree rooting, gene tree topological uncertainty, multiple optimal reconciliations...
  • VBCTOOL

  • Referenced in 1 article [sw14654]
  • designed to draw binary and general rooted trees, as they occur during an algorithmic process...
  • Nenofex

  • Referenced in 18 articles [sw09579]
  • formula in NNF is represented as a tree with structural restrictions in order to keep ... small and distances from nodes to the root short. Expansions of variables are scheduled based...