12.2.1 Using alignment masks

To exclude certain sites or regions of your alignment before tree building, you can apply Masked-type annotations to an alignment’s consensus sequence. Masked-type annotations can be applied manually, or using the Mask Alignment option under the Tools menu (see section 9.4 ). This tool enables you to either annotate masked sites, or make a copy of the alignment with masked sites removed. If you choose to annotate masked sites, these can be removed for tree building by checking Exclude masked sites in the Tree building options. With this option, any sites covered by Masked-type annotations will not be used when the tree is inferred but will be retained on the alignment.

Masked-type annotations can be either directly on the consensus sequence of the alignment, or on one or more tracks. If you have multiple tracks containing Masked annotations, you need to select the track you want to use in the Exclude masked sites option. In this way, you can use multiple masks to compare trees inferred from different subsets of your alignments (e.g., excluding different codon positions, or excluding fast-evolving sites). Only the track used to exclude masked sites when inferring the tree will be included in the Alignment View once the tree is built (see section 12.5 )