Distance-based methods
The "Create tree" tool can be used to generate a distance-based phylogenetic tree with multiple alignments as input:
Toolbox | Classical Sequence Analysis (
) | Alignments and Trees (
)| Create Tree (
)
This will open the dialog displayed in figure 21.2:
If an alignment was selected before choosing the Toolbox action, this alignment is now listed in the Selected Elements window of the dialog. Use the arrows to add or remove elements from the Navigation Area. Click Next to adjust parameters.
Figure 21.3: Adjusting parameters for distance-based methods.
Figure 21.3 shows the parameters that can be set for this distance-based tree creation:
- Tree construction
- Tree construction algorithm
- The UPGMA method. Assumes constant rate of evolution.
- The Neighbor Joining method. Well suited for trees with varying rates of evolution.
- Nucleotide distance measure
- Jukes Cantor. Assumes equal base frequencies and equal substitution rates.
- Kimura 80. Assumes equal base frequencies but distinguishes between transitions and transversions.
- Protein distance measure
- Jukes Cantor. Assumes equal amino acid frequency and equal substitution rates.
- Kimura protein. Assumes equal amino acid frequency and equal substitution rates. Includes a small correction term in the distance formula that is intended to give better distance estimates than Jukes Cantor.
- Tree construction algorithm
- Bootstrapping.
- Perform bootstrap analysis. To evaluate the reliability of the inferred trees, CLC Genomics Workbench allows the option of doing a bootstrap analysis (see Bootstrap tests). A bootstrap value will be attached to each node, and this value is a measure of the confidence in the subtree rooted at the node. The number of replicates in the bootstrap analysis can be adjusted in the wizard by specifying the number of times to resample the data. The default value is 100 resamples. The bootstrap value assigned to a node in the output tree is the percentage (0-100) of the bootstrap resamples which resulted in a tree containing the same subtree as that rooted at the node.
For a more detailed explanation, see Bioinformatics explained.