Features

The Phylogeny Modulewith a greatly enhanced viewer for visualizing and working with phylogenetic trees. The viewer allows the user to rapidly create high-quality, publication-ready figures of phylogenetic trees. Large trees are made easy to explore using different zoom functionalities and a small minimap of the entire tree. The viewer also comes with two alternative tree layouts, namely circular layouts and radial layouts, which are great for visualizing very large trees. Finally, the new viewer supports importing, editing and visualization of metadata associated with nodes in phylogenetic trees. The Phylogeny Modulescheduled to become part of the CLC Main Workbench and the CLC Genomics Workbench in the near future.

In addition to the new viewer, two new tools are included in the module. The first tool can reconstruct phylogenetic trees based on k-mers. This approach avoids the computationally intensive step of constructing a multiple alignment of the input sequences. However the accuracy of the constructed tree might not be as high as the other reconstruction methods. The k-mer based reconstruction tool is especially useful for whole genome phylogenetic reconstruction where the genomes are closely releated, i.e. they differ mainly by SNPs and contain no or few structural variations. The second new tool implements a statistic evaluation of different substitution models to be used with maximum likelihood tree construction, similar to that produced by the tool Model Testing[Posada and Crandall, 1998]. The output of this tool is a report that lists the recommended settings to be used when constructing phylogenetic trees based on maximum likelihood. Below is an overview of these tools and the main features of the new editor. Further details can be found in the subsequent sections.

• Phylogenetic tree editor.
  • Circular and radial layouts.
  • Import of metadata in Excel and CSV format.
  • Tabular view of metadata with support for editing.
  • Options for collapsing nodes based on bootstrap values.
  • Re-ordering of tree nodes.
  • Legends describing metadata.
  • Visualization of metadata though e.g. node color, node shape, branch color, etc.
  • Minimap navigation.
  • Coloring and labeling of subtrees.
  • Curved edges.
  • Editable node sizes and line width.
  • Intelligent visualization of overlapping labels and nodes.

• K-mer based tree construction.
  • Construction of phylogenetic trees without a time consuming multiple alignment of the input sequences [Blaisdell, 1989].

• Model Testing.
  • Tool for selecting a substitution model for use with maximum likelihood tree construction.
  • Supports comparison of five substitution models (Jukes-Cantor, Felsenstein 81, Kimura 80, Hasegawa-Kishino-Yano, General Time Reversible), optional rate variation and topology variation.
  • Compares models based on hierarchical likelihood ratio tests, Bayesian information criterion and Akaike minimum theoretical information criterion.