ArticleMolecular biology and evolution2017
A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
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- The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases.Communications biology · 2023Article
- The role of junctophilin proteins in cellular function.Physiological reviews · 2022Review
- Integrated analysis of necroptosis-related genes for evaluating immune infiltration and colon cancer prognosis.Frontiers in immunology · 2022Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- Article
- Expression and Function of Host Defense Peptides at Inflammation Sites.International journal of molecular sciences · 2019Review
- An expanded molecular phylogeny of Plumbaginaceae, with emphasis onEcology and evolution · 2018Article
- The Biological Object Notation (BON): a structured file format for biological data.Scientific reports · 2018Article
- HybSuite: An integrated pipeline for hybrid capture phylogenomics from reads to trees.Applications in plant sciencesArticle
Corrections and comments
- Erratum issuedErratum.2017
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.