Dec 25, 2015

Do Phylogenetic Tree Viewers correctly display Support Values?

BioRxiv : the Preprint Server for Biology
Lucas Czech, Jaime Huerta-Cepas

Abstract

Phylogenetic trees are routinely visualized to present and interpret the evolutionary relationships of the species that are being studied. Virtually all empirical evolutionary data studies contain a visualization of the inferred tree with support values using one of the popular and highly cited (e.g., TreeView, Dendroscope, FigTree, Archaeopteryx, etc.) tree viewing tools. As a consequence, programming errors or ambiguous semantics in tree file formats can lead to erroneous tree visualizations and consequently incorrect interpretations of phylogenetic analyses. Here, we discuss the problems that can and do arise when displaying branch support values on trees. Presumably for historical reasons, branch support values (e.g., bootstrap support or Bayesian posterior probabilities) are typically stored as node labels in the widely-used Newick tree format. However, support values are attributes of branches (bipartitions) in unrooted phylogenetic trees. Therefore, storing support values as node labels can potentially lead to incorrect support-value-to-bipartition mappings when re-rooting trees in tree viewers. This depends on the mostly implicit semantics of tree viewers for interpreting node labels. To assess the potential impact of t...Continue Reading

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Mentioned in this Paper

Study
Trees (plant)
Phylogenetic Analysis
Bio-Informatics
Dorsal
Species
Analysis
Branching (Qualifier Value)
Anatomic Node

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