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 (Image gene_and_protein_analysis) | Alignments and Trees (Image alignmentsandtrees)

To generate a distance-based phylogenetic tree choose:

        Create Tree (Image tree)

and to generate a maximum likelihood based phylogenetic tree choose:

        Maximum Likelihood Phylogeny (Image ml_tree)

In both cases the dialog displayed in figure 21.1 will be opened:

Image treedialog
Figure 21.1: Creating a Tree.

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.