CLC Phylogeny Module is an upgrade to the existing phylogeny tools. The plugin is available in CLC Main Workbench 6.9 and CLC Genomics Workbench 6.5.
The Phylogeny Module comes with 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 the 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.
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. The k-mer based reconstruction tool is especially useful for whole genome phylogenetic reconstruction where the genomes are closely related.
The second new tool implements a statistic evaluation of different substitution models to be used with maximum likelihood tree construction. The output of this tool is a report that lists the recommended settings to be used when constructing phylogenetic trees based on maximum likelihood.
The new tools can also be run on a CLC Genomics Server by installing the server version of the plugin.
The Phylogeny Module is only available if you have the current versions of CLC Genomics Workbench 6.5 or CLC Main Workbench 6.9.
Bug fixes - v1.0.1
- Fixed a bug where a right click outside a meta data table would result in the meta data context menu popping up.
- Fixed a bug which could make it impossible to save view settings or apply saved settings.
- The tree view now behaves correctly when two trees are open at the same time.
New features - v1.0
- Two new distance measures was added to K-mer based tree construction. The "Mahalanobis" and the "Fractional common K-mer count" distance measures.
- Added an option for using the Kimura 80 substitution model when creating trees with distance based methods.
- Distance based tree reconstruction methods can now reconstruct trees from protein alignments using the Jukes-Cantor substitution model or the Kimura protein ML distance estimate.
- A user defined start tree can now be supplied to the ML inference tool.
- Subtrees can now be labled with a custom text.
- Subtrees and individual nodes can be completely hidden.
- The root of a tree can now be hidden.
- Reset button which resets the tree topology and the node order.
- Font for bootstrap values and branch lengths can now be controlled manually.
- Highlighting of branches where the bootstrap value is above a user defined threshold.
- Metadata can now be visualized using one or more color-code layers next to leaf nodes.
- Metadata can now be visualized through node sizes and shapes.
- Node Metadata can be created and modified using the right click menu in the tree view.
Improvements - v1.0
- Two-way synchronization of selections in the tree view and the meta data table.
- The metadata importer now logs all imported entries where the match was not exact.
- The side panel layout has been changed and it is now faster to navigate to the function you need.
- Background of node labels can be made transparent.
- An option to show all labels, even if they overlap, has been introduced.
- Improved filtering on numerical metadata categories.
- Automatic panning of the tree view when selecting an entry in the metadata table.
- Visualization options controlled by metadata are now grayed out.
- A warning is now shown when users try to generate a large multiple alignment from the right click menu in the tree view.
- Legend boxes can now be resized.
- Bootstrap values can now be reused when a tree is re-rooted.
- Reduced the memory requirements of K-mer based tree construction
Bug fixes - v1.0
- Several bug fixes related to panning and zooming in the tree-view.
- Fixed various bugs related to undo redo functionality.
- Fixed bugs in progressbar for several tools.
Changes - v1.0
- Bootstrap values are now shown in percent.