Abstract
Phylogenetic trees are routinely visualized to present and interpret the evolutionary relationships of species. Virtually all empirical evolutionary data studies contain a visualization of the inferred tree with support values. Ambiguous semantics in tree file formats can lead to erroneous tree visualizations and therefore to incorrect interpretations of phylogenetic analyses.
Here, we discuss problems that can and do arise when displaying branch support values on trees after re-rooting. Branch support values are typically stored as node labels in the widely-used Newick tree format. However, support values are attributes of branches. Storing them as node labels can yield errors when re-rooting trees. This depends on the mostly implicit semantics that tools deploy to interpret node labels. We reviewed 10 tree viewers and 7 bioinformatics toolkits that can re-root trees. We found that 12 out of 17 of these tools did not permit users choosing the semantics of node labels. Thus, unaware users might get incorrect results when rooting trees produced by common phylogenetic inference programs. We illustrate such an incorrect mapping through several test cases and real examples taken from the literature. This review has led to improvements and workarounds in 5 of the tested tools. We suggest tools should provide an option that explicitly forces users to define the semantics of branch support values.
