Dendroscope: An interactive viewer for large phylogenetic trees

Christian Rausch,Markus Franz,Daniel H Huson,Daniel C Richter,Tobias Dezulian,Regula Rupp

doi:10.1186/1471-2105-8-460

Abstract

BackgroundResearch in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems.ResultsWe have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP.ConclusionDendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets.

Highlights

Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example
Phylogenetic trees are used to represent evolutionary relationships between biological taxa, while taxonomical hierarchies such as the NCBI taxonomy are used to structure the wealth of molecular sequence data
While TreeJuxtaposer is the tool of choice for very large datasets, it has limited value as an allround tree visualization tool, as it only implements one particular tree view, it lacks basic graphics export capabilities and it does not allow one to save and reopen a modified tree

Summary

Introduction

Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. A large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. While TreeJuxtaposer is the tool of choice for very large datasets (containing hundreds of thousands of taxa), it has limited value as an allround tree visualization tool, as it only implements one particular tree view (namely the rectangular phylogram, perhaps because this is the only view that is useful for large trees), it lacks basic graphics export capabilities and it does not allow one to save and reopen a modified tree

Objectives

Methods

Results