A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits. (22nd March 2017)

• Record Type: Journal Article
• Authors: Czech, Lucas; Huerta-Cepas, Jaime; Stamatakis, Alexandros
• Is Part Of: Molecular biology and evolution. Volume 34:Number 6(2017:Jun.)
• Page Start: 1535
• Page End: 1542
• Publication Date: 2017-03-22
• Subjects: phylogenetic trees -- tree visualization -- tree viewers -- bioinformatics toolkits -- Newick format -- branch support values -- branch labels -- software -- bugs; Molecular biology -- Periodicals; Molecular evolution -- Periodicals; Evolution, Molecular -- Periodicals; Molecular Biology -- Periodicals; 572.8
• DOI: 10.1093/molbev/msx055
• Languages: English
• ISSNs: 0737-4038

Abstract

Abstract: Phylogenetic trees are routinely visualized to present and interpret the evolutionary relationships of species. Most empirical evolutionary data studies contain a visualization of the inferred tree with branch 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 arise when displaying branch values on trees after rerooting. Branch values are typically stored as node labels in the widely-used Newick tree format. However, such values are attributes of branches. Storing them as node labels can therefore yield errors when rerooting trees. This depends on the mostly implicit semantics that tools deploy to interpret node labels. We reviewed ten tree viewers and ten bioinformatics toolkits that can display and reroot trees. We found that 14 out of 20 of these tools do not permit users to select the semantics of node labels. Thus, unaware users might obtain incorrect results when rooting trees. We illustrate such incorrect mappings for several test cases and real examples taken from the literature. This review has already led to improvements in eight tools. We suggest tools should provide options that explicitly force users to define the semantics of node labels.