Phylogenetics describes the taxonomic classification of organisms based on their evolutionary history i.e. their phylogeny. Phylogenetics is therefore an integral part of the science of systematics that aims to establish the phylogeny of organisms based on their characteristics. Furthermore, phylogenetics is central to evolutionary biology as a whole as it is the condensation of the overall paradigm of how life arose and developed on earth. The focus of this module is the reconstruction and visualization of phylogenetic trees. Phylogenetic trees illustrate the inferred evolutionary history of a set of organisms, and makes it possible to e.g. identify groups of closely related organisms and observe clustering of organisms with common traits. See 21.4.1 for a more detailed introduction to phylogenetic trees.
The viewer for visualizing and working with phylogenetic trees allows the user to create high-quality, publication-ready figures of phylogenetic trees. Large trees can be explored in two alternative tree layouts; circular and radial. The viewer supports importing, editing and visualization of metadata associated with nodes in phylogenetic trees.
Below is an overview of the main features of the phylogenetic tree editor. Further details can be found in the subsequent sections.
Main features of the 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.
For a given set of aligned sequences (see Create an alignment) it is possible to infer their evolutionary relationships. In CLC Genomics Workbench this may be done either by using a distance based method or by using maximum likelihood (ML) estimation, which is a statistical approach (see Bioinformatics explained). Both approaches generate a phylogenetic tree.
Three tools are available for generating phylogenetic trees:
- K-mer Based Tree Construction () Is a distance-based method that can create trees based on multiple single sequences. K-mers are used to compute distance matrices for distance-based phylogenetic reconstruction tools such as neighbor joining and UPGMA (see Distance-based methods). This method is less precise than the Create Tree tool but it can cope with a very large number of long sequences as it does not require a multiple alignment. The k-mer based tree construction 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.
- Maximum Likelihood Phylogeny () The most advanced and time consuming method of the three mentioned. The maximum likelihood tree estimation is performed under the assumption of one of five substitution models: the Jukes-Cantor, the Kimura 80, the HKY and the GTR (also known as the REV model) models (see Maximum Likelihood Phylogeny for further information about the models). Prior to using the Maximum Likelihood Phylogeny tool for creating a phylogenetic tree it is recommended to run the Model Testing tool in order to identify the best suitable models for creating a tree.
- Create Tree () Is a tool that uses distance estimates computed from multiple alignments to create trees. The user can select whether to use Jukes-Cantor distance correction or Kimura distance correction (Kimura 80 for nucleotides/Kimura protein for proteins) in combination with either the neighbor joining or UPGMA method (see Distance-based methods).
- K-mer Based Tree Construction
- Create tree
- Model Testing
- Maximum Likelihood Phylogeny
- Tree Settings
- Metadata and phylogenetic trees