ArticleBMC bioinformatics2021
Root Digger: a root placement program for phylogenetic trees.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Triplet-based species tree estimation: Sensitivity to gene tree rooting (or lack thereof).PLoS computational biology · 2026Article
- CAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution.Systematic biology · 2026Article
- nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models.Journal of molecular evolution · 2025Article
- Population genomics of seal lice provides insights into the postglacial history of northern European seals.Molecular ecology · 2024Article
- Reliable estimation of tree branch lengths using deep neural networks.PLoS computational biology · 2024Article
- Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites.Journal of integrative bioinformatics · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Biodegradation of Inosine and Guanosine byInternational journal of molecular sciences · 2023Article
- Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.Genome biology and evolution · 2023Article
- Phylogenomic Testing of Root Hypotheses.Genome biology and evolution · 2023Article
- DISCO+QR: rooting species trees in the presence of GDL and ILS.Bioinformatics advances · 2023Article
- nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.Systematic biology · 2022Article
- Quintet Rooting: rooting species trees under the multi-species coalescent model.Bioinformatics (Oxford, England) · 2022Article
- Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals.Systematic biology · 2022Article
- Orthology Clusters from Gene Trees with Possvm.Molecular biology and evolution · 2021Article
- Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult.Molecular biology and evolution · 2021Article
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2 authors.
Funding
Abstract
backgroundIn phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as molecular clock analysis (including midpoint rooting) or rooting the tree using an outgroup. Non-reversible Markov models can also be used to compute the likelihood of a potential root position.
resultsWe present a software called RootDigger which uses a non-reversible Markov model to compute the most likely root location on a given tree and to infer a confidence value for each possible root placement. We find that RootDigger is successful at finding roots when compared to similar tools such as IQ-TREE and MAD, and will occasionally outperform them. Additionally, we find that the exhaustive mode of RootDigger is useful in quantifying and explaining uncertainty in rooting positions.
conclusionsRootDigger can be used on an existing phylogeny to find a root, or to asses the uncertainty of the root placement. RootDigger is available under the MIT licence at https://www.github.com/computations/root_digger .
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