Metadata and phylogenetic trees
When a tree is reconstructed, some mandatory metadata will be added to nodes in the tree. These metadata are special in the sense that the tree viewer has specialized features for visualizing the data and some of them cannot be edited. The mandatory metadata include:
- Node name The node name.
- Branch length The length of the branch, which connects a node to the parent node.
- Bootstrap value The bootstrap value for internal nodes.
- Size The length of the sequence which corresponds to each leaf node. This only applies to leaf nodes.
- Start of sequence The first 50bp of the sequence corresponding to each leaf node.
To view metadata associated with a phylogenetic tree, click on the table icon (
) at the bottom of the tree. If you hold down the Ctrl key (or 
on Mac) while clicking on the table icon (), you will be able to see both the tree and the table in a split view (figure 22.22).
Figure 22.22: Tabular metadata that is associated with an existing tree shown in a split view. Note that Unknown written in italics (black branches) refer to missing metadata, while Unknown in regular font refers to metadata labeled as "Unknown".
Additional metadata can be associated with a tree by clicking the Import Metadata button. This will open up the dialog shown in figure 22.23.
To associate metadata with an existing tree a common denominator is required. This is achieved by mapping the node names in the "Name" column of the metadata table to the names that have been used in the metadata table to be imported. In this example the "Strain" column holds the names of the nodes and this column must be assigned "Name" to allow the importer to associate metadata with nodes in the tree.
It is possible to import a subset of the columns in a set of metadata. An example is given in figure 22.23. The column "H" is not relevant to import and can be excluded simply by leaving the text field at the top row of the column empty.
Figure 22.23: Import of metadata for a tree. The second column named "Strain" is choosen as the common denominator by entering "Name" in the text field of the column. The column labeled "H" is ignored by not assigning a column heading to this column.
Subsections
- Table Settings and Filtering
- Add or modify metadata on a tree
- Undefined metadata values on a tree
- Selection of specific nodes