Phylogenetic trees frequently include information associated with the internal nodes or branches of the tree. For example, the following phylogeny of reptiles has bootstrap values associated with its branches and has higher taxonomic level names (e.g., Amniotes, Archosaurs) on internal nodes.
This information can be included in the Nexus and Newick plain text tree files. However, these formats do not distinguish between values that should be displayed on internal nodes and those that should be associated with internal branches. Therefore, when you import these formats into Geneious, you will be asked to specify whether attributes should be treated as branch support values or node labels.
Effect of Assigning Support Values to Branches or Nodes
Properly rooting a tree is usually the first step after creating or importing it, as the initial position of the root is often arbitrary due to the nature of most tree inference methods. Because values associated with internal nodes and branches behave differently when a tree is re-rooted, Geneious needs to know whether these values are node support values or branch labels in order to correctly place them on the re-rooted tree.
For example, consider the following tree of primates. The tree on the left (a) has been arbitrarily rooted on the Humans branch instead of the Other mammals branch. Note the bootstrap support value of 85% for the split (branch) separating Humans and Chimps from the remaining taxa, which, although the position of the root is misleading, represents support for the Humans + Chimps clade (Hominini). By treating the bootstrap support values as branch support, when the tree is re-rooted on the Other mammals branch in the tree on the right (b), the 85% bootstrap value correctly stays on the branch separating Humans and Chimps from the other taxa, now located next to the Hominini node.
Primates tree a) arbitrarily on the Humans branch b) correctly re-rooted with the Other mammals branch.
If we had instead treated bootstrap support as a node-associated value, re-rooting the tree would have associated bootstrap values with the wrong nodes, as in the tree below. In this case, the 85% bootstrap support value appears on the Great Apes node, giving the impression that it represents support for the wrong clade (i.e. Great Apes), rather than Hominini.
Primates tree re-rooted on the Other mammals branch, with bootstrap values in the wrong places, due to being associated with nodes rather than branches.