Inferring phylogenetic trees
For a given set of aligned sequences (see Sequence alignment) it is possible to infer their evolutionary relationships. In CLC Genomics Workbench this may be done either by using a distance based method (see Bioinformatics explained.) or by using the statistically founded maximum likelihood (ML) approach [Felsenstein, 1981]. Both approaches generate a phylogenetic tree. The tools are found in:
Toolbox | Classical Sequence Analysis (
) | Alignments and Trees (
)
To generate a distance-based phylogenetic tree choose:
Create Tree (
)
and to generate a maximum likelihood based phylogenetic tree choose:
Maximum Likelihood Phylogeny (
)
In both cases the dialog displayed in figure 21.1 will be opened:
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.
Subsections