Maximum Likelihood Phylogeny

To generate a maximum likelihood based phylogenetic tree, go to:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | Alignments and Trees (Image alignmentsandtrees)| Maximum Likelihood Phylogeny (Image ml_tree)

First, select the alignment to be used for the reconstruction (figure 25.7).

Image ml_tree_step2_v2
Figure 25.7: Select the alignment for tree construction.

You can then set up the following parameters (figure 25.8):

Image ml_tree_step3
Figure 25.8: Adjusting parameters for maximum likelihood phylogeny

In the next step of the wizard it is possible to perform bootstrapping (figure 25.9).

Image ml_tree_step4
Figure 25.9: Adjusting parameters for ML phylogeny

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.