• PhySIC

  • Referenced in 8 articles [sw08376]
  • PhySIC: A Veto Supertree Method with Desirable Properties. This paper focuses on veto supertree methods ... trees. We propose desirable properties that a supertree should satisfy in this framework, namely ... property (PI). The former requires that the supertree does not contain relationships that contradict ... that all topological information contained in the supertree is present in a source tree...
  • SPRSupertrees

  • Referenced in 10 articles [sw14683]
  • Supertrees is a software package for computing supertrees that minimize the SPR distance. SPR Supertrees...
  • Quartets MaxCut

  • Referenced in 5 articles [sw29616]
  • maximum of few dozens of taxa. Supertree methods construct a large tree over a large ... half different species, the use of a supertree method over the product of accurate methods ... previously been most successful in dealing with supertrees. Our algorithm is based on a divide...
  • FlipCut

  • Referenced in 2 articles [sw08374]
  • FlipCut supertrees: towards matrix representation accuracy in polynomial time. In computational phylogenetics, supertree methods provide ... clades of the Tree of Life. The supertree problem can be formalized in different ways ... some graph. Matrix representation methods compute supertrees of superior quality, but the underlying optimization problems ... based methods have polynomial running time, but supertrees are inferior in quality. In this paper...
  • SuperFine

  • Referenced in 2 articles [sw29605]
  • SuperFine: fast and accurate supertree estimation. Many research groups are estimating trees containing anywhere from ... with more than a few thousand sequences. Supertree methods, which assemble phylogenetic trees from ... improve the accuracy and scalability of supertree methods. Our study, using both simulated and empirical ... data, shows that SuperFine-boosted supertree methods produce more accurate trees than standard supertree methods...
  • SuperTriplets

  • Referenced in 3 articles [sw29604]
  • SuperTriplets: a triplet-based supertree approach to phylogenomics. Motivation: Phylogenetic tree-building methods use molecular ... propose less resolved but more reliable supertrees than those inferred using Matrix Representation with Parsimony...
  • EPoS

  • Referenced in 4 articles [sw08375]
  • construction, consensus trees and various graph-based supertree methods. The rendering system can be customized...
  • L.U.St

  • Referenced in 1 article [sw29608]
  • tool for approximated maximum likelihood supertree reconstruction. Background: Supertrees combine disparate, partially overlapping trees ... attained from the inspection of individual phylogenies. Supertrees can be seen as meta-analytical tools ... taxon-dense phylogenies. Further to that, supertrees have found applications in phylogenomics where they ... python tool for approximate maximum likelihood supertree inference and illustrate its application using a genomic...
  • FastRFS

  • Referenced in 1 article [sw29617]
  • FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization. Motivation: The estimation ... scale well to even moderate-sized datasets. Supertree methods, which are used to construct trees ... phylogenies for large and potentially heterogeneous datasets. Supertree estimation is itself NP-hard ... current supertree method has sufficient accuracy and scalability to provide good accuracy on the large...
  • Triplet MaxCut

  • Referenced in 1 article [sw29615]
  • Triplet MaxCut: a new toolkit for rooted supertree. The rapid increase of molecular, as well ... combine this data into a unified hypothesis. Supertree methods are essential when amalgamating phylogenetic information ... single tree. The goal of a supertree algorithm is to satisfy maximally each such source ... MaxCut (TMC), performing various operations in rooted supertree, principally amalgamating rooted trees based on amalgamating...
  • PhyloWS

  • Referenced in 2 articles [sw08275]
  • Bininda-Emonds (ed.), Phylogenetic supertrees. Combining information to reveal the tree of life. Dordrecht: Kluwer...
  • CLANN

  • Referenced in 1 article [sw23047]
  • Clann: investigating phylogenetic information through supertree analyses. Clann has been developed in order to provide ... investigating phylogenetic information through the application of supertrees. AVAILABILITY: Clann has been precompiled for Linux...
  • SIESTA

  • Referenced in 1 article [sw29618]
  • SIESTA: Enhancing searches for optimal supertrees and species trees. Background: Many supertree estimation and multi...
  • supersmartR

  • Referenced in 1 article [sw28959]
  • hybrid method using both the supermatrix and supertree approach. supersmartR is a project aimed...
  • DACTAL

  • Referenced in 1 article [sw29613]
  • full taxon set using a new supertree method. We prove that DACTAL is guaranteed...
  • SageMath

  • Referenced in 1538 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • Gringo

  • Referenced in 94 articles [sw04630]
  • This document provides an introduction to the Answer...
  • Gecode

  • Referenced in 60 articles [sw06272]
  • Gecode is a toolkit for developing constraint-based...
  • Potassco

  • Referenced in 66 articles [sw06996]
  • Potassco: the Potsdam answer set solving collection. This...