ArticleMolecular biology and evolution2021
Log Transformation Improves Dating of Phylogenies.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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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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Who cites it
8 citing papers in PubMed.
- Drivers of Population Genetic Diversity Across Ecologically Distinct Species in a Cape Fynbos Grass Clade.Molecular ecology · 2026Article
- The association of thyroid peroxidase antibodies with microvascular invasion in patients with papillary thyroid carcinoma.European journal of medical research · 2025Article
- Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model.Systematic biology · 2024Article
- Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock.Genome biology and evolution · 2024Review
- Maximum likelihood phylogeographic inference of cell motility and cell division from spatial lineage tracing data.Bioinformatics (Oxford, England) · 2024Article
- Wilson and Sarich (1969): The birth of a molecular evolution research paradigm.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- DaTeR: error-correcting phylogenetic chronograms using relative time constraints.Bioinformatics (Oxford, England) · 2023Article
- Hypoconnectivity of the Amygdala in Patients with Low-Back-Related Leg Pain Linked to Individual Mechanical Pain Sensitivity: A Resting-State Functional MRI Study.Journal of pain research · 2023Article
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Authors and funding
2 authors.
Funding
Abstract
Phylogenetic trees inferred from sequence data often have branch lengths measured in the expected number of substitutions and therefore, do not have divergence times estimated. These trees give an incomplete view of evolutionary histories since many applications of phylogenies require time trees. Many methods have been developed to convert the inferred branch lengths from substitution unit to time unit using calibration points, but none is universally accepted as they are challenged in both scalability and accuracy under complex models. Here, we introduce a new method that formulates dating as a nonconvex optimization problem where the variance of log-transformed rate multipliers is minimized across the tree. On simulated and real data, we show that our method, wLogDate, is often more accurate than alternatives and is more robust to various model assumptions.
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Registered trials
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