Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks.

@article{Huson2012Dendroscope3A,
  title={Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks.},
  author={Daniel H. Huson and C{\'e}line Scornavacca},
  journal={Systematic biology},
  year={2012},
  volume={61 6},
  pages={
          1061-7
        }
}
Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks. It provides a number of methods for drawing and comparing rooted phylogenetic networks, and for computing them from rooted trees. The program can be used interactively or in command-line mode. The program is written in Java, use of the software is free, and installers for all 3 major operating systems can be downloaded from www.dendroscope.org. [Phylogenetic trees; phylogenetic networks; software.]. 

Figures from this paper

A new algorithm to construct phylogenetic networks from trees.

  • J. Wang
  • Computer Science
    Genetics and molecular research : GMR
  • 2014
TLDR
It is shown that QuickCass can construct simpler phylogenetic networks than BIMLR and is a polynomial-time algorithm when the output network that is constructed by QuickCass is binary.

A Survey of Methods for Constructing Rooted Phylogenetic Networks

TLDR
This paper will discuss and compare these methods by both the practical and artificial datasets, in the aspect of the running time of the methods and the effective of constructed phylogenetic networks.

IGNet: Constructing Rooted Phylogenetic Networks Based on Incompatible Graphs

TLDR
Besides the on-line computation service, the IGNet also provides downloadable Java programs of Open image in new window and BIMLR for off-line construction of rooted phylogenetic networks.

Do Phylogenetic Tree Viewers correctly display Support Values

TLDR
The problems that can and do arise when displaying branch support values on trees are discussed and it is suggested that branch supportvalues should exclusively be stored as meta-data associated to branches (and not nodes), and if this is not feasible, tree viewers should include a user dialogue that explicitly forces users to define if node labels shall be interpreted as node or branch labels, prior to tree visualization.

Phylostat: a web-based tool to analyze paralogous clade divergence in phylogenetic trees

TLDR
Here, Phylostat is a web-based tool built on phylo.io to allow comparative clade divergence analysis, which is available at https://phylost at.adebalilab.org under an MIT open-source licence.

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

TLDR
The Environment for Tree Exploration v3 is presented, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics.

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

TLDR
ITOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format, and its account system has been redesigned to simplify the management of trees in user-defined workspaces and projects.

Lnetwork: an efficient and effective method for constructing phylogenetic networks

TLDR
An improved Cass algorithm is introduced, Lnetwork, which can construct a phylogenetic network for a given set of clusters and is shown to be significantly faster than Cass and effectively weakens the influence of input data order.

Inferring Phylogenetic Networks Using PhyloNet

TLDR
PhyloNet now allows for maximum parsimony, maximum likelihood, and Bayesian inference of phylogenetic networks from gene tree estimates, andBayesian inference directly from sequence data (sequence alignments or bi-allelic markers) is implemented.
...

References

SHOWING 1-10 OF 40 REFERENCES

Drawing Rooted Phylogenetic Networks

  • D. Huson
  • Biology
    IEEE/ACM Transactions on Computational Biology and Bioinformatics
  • 2009
TLDR
This paper discusses the problem of drawing rooted phylogenetic networks as cladograms or phylograms in a number of different views that are commonly used for rooted trees.

Dendroscope: An interactive viewer for large phylogenetic trees

TLDR
Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets, and is optimized to run interactively on trees containing hundreds of thousands of taxa.

Summarizing Multiple Gene Trees Using Cluster Networks

TLDR
The concept of a cluster network that can be used to combine such trees into a single rooted network, which can be drawn either as a cladogram or phylogram is introduced.

Phylogenetic super-networks from partial trees

TLDR
This paper poses the problem of inferring a phylogenetic super-network from incomplete phylogenetic data and provides an efficient algorithm for doing so, called the Z-closure method, which is implemented as a plug-in for the program SplitsTree4.

Neighbor-net: an agglomerative method for the construction of phylogenetic networks.

TLDR
Neighbor-Net is presented, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei and can quickly produce detailed and informative networks for several hundred taxa.

Comparison of Tree-Child Phylogenetic Networks

TLDR
An injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors are provided, and this representation is used to define a distance on this class that extends the well-known Robinson-Foulds distance for phylogenetic trees and to give an alignment method for pairs of networks in this class.

Tanglegrams for rooted phylogenetic trees and networks

TLDR
This article presents the first formal definition of a tanglegram for rooted phylogenetic networks and presents a heuristic approach for computing one, called the NN-tanglegram method.

PADRE: a package for analyzing and displaying reticulate evolution

TLDR
The software package PADRE (Package for Analyzing and Displaying Reticulate Evolution) is described, allowing the reconstruction of complex evolutionary histories for polyploids in the form of phylogenetic networks.

A classification of consensus methods for phylogenetics

TLDR
This paper surveys the main consensus tree methods used in phylogenetics, and explores the links between the different methods, producing a classification of consensus Tree methods.

Extended Newick: it is time for a standard representation of phylogenetic networks

TLDR
The adoption of the extended Newick format as a standard for the representation of phylogenetic network is an important step towards the publication of explicit phylogenetics networks in peer-reviewed journals and their incorporation in a future database of published phylogenetic networks.