Dendroscope: An interactive viewer for large phylogenetic trees

We 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.Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets.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. The size of trees under consideration is growing larger and larger.The Tree of Life project [1], which aims at reconstructing the evolutionary relationship of all living species on earth, now considers more than 11,000 species. The Ribosomal Database Project II provides a hierarchical browser for a collection of approximately 340,000 ribosomal RNA sequences. Recent metagenomic analysis software [2] makes use of the full NCBI taxonomy, which now contains more than 390,000 taxa, to estimate the taxonomical content of a dataset.Most currently available tree viewers are designed to handle trees containing up to a few thousand nodes. A notable exception is TreeJuxtaposer [3], which was explicitly designed to visualize large trees. While TreeJuxtaposer is the tool of choice for very large datasets (containing hundreds of thousands of taxa), it has limited value as an all-round 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