Bioinformatics Genome Annotation Phylogenetic analysis


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Researchers studying phylogenetic relationships need software that is able to visualize rooted phylogenetic trees and networks efficiently, increasingly either of small or large datasets to their phylogenetic trees and data, involving hundreds of thousands of taxa. A software or module has been developed for the independent tree and rooted network viewer “Dendroscope that addresses these issues. This has been written in Java. It takes input of phylogenetic trees and networks in the format of Newick, Nexus. It provides 8 different tree views, e.g. phylogram, cladogram or radial views. It provides many tree manipulating functions like re-rooting, subtree rotating, tree flipping and formatting features like renaming, coloring or resizing edges, nodes and labels.

The program should be user friendly and can be run on every operating system, facilitate interactive browsing and editing the trees and allow one to export the result in multiple file formats in publication quality. Moreover, this tool is available with a graphical user interface (GUI) or a command line interface (CLI), depending on the use of the users.

The Main window is used to display the taxonomy and to control the program through the main menus which includes file, layout, edit, select, options, algorithms, view, toolbar, status line, window menus etc which helps in increasing the functionality of Dendroscope. 

Feature List:

  • Large trees with hundreds of thousands of taxa can be easily displayed, browsed and edited
  • Multiple trees and networks from a single file can be displayed together in an m by n grid
  • Novel magnifying features for zooming detailed views (see screenshots)
  • Find and replace tool bar that uses regular expressions
  • Subtrees can be collapsed and colored
  • All labels (leaves/inner nodes and edges) can be edited
  • Trees can be rerooted
  • Seven different views are available, including a rectangular, slanted, circular and radial view
  • Input formats: Newick and Nexus, extended-Newick (for rooted phylogenetic networks) and Dendroscope
  • Multiple graphic export formats: .eps, .svg, .png, .jpg, .gif, .bmp, .pdf
  • Trees and networks can be copied and pasted between different windows
  • Platform independent 
  • Consensus trees and rooted phylogenetic networks can be computed from a set of trees
  • Hybridization networks and tanglegrams for multifurcating trees on unequal taxon sets
  • Command line mode for easy use

The evolutionary history of a set of taxa, such as genes or species, is usually depicted as a rooted phylogenetic tree in Dendroscope results depiction. Rooted phylogenetic networks provide a generalization of rooted phylogenetic trees that can be used to explicitly represent reticulate events or to visualize incompatibilities in a data set. A rooted phylogenetic network is shown as a directed acyclic graph in which each leaf is labeled by a unique taxon and that has precisely one node that is the ancestor of all other nodes, called the root. Any node with more than 1 parent is called a reticulation and the edges leading into such a node are called reticulate edges.

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