ArticlePLoS computational biology2023
LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses.
Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Bayesian credible sets for phylogenetic tree topologies with applications to coverage analysis and cross-model comparison.Molecular biology and evolution · 2026Article
- Testing the validity and adequacy of linguistic phylogenetic analyses.PLoS computational biology · 2026Article
- Bayesian Model Averaging of Parametric Coalescent Models for Phylodynamic Inference.Molecular biology and evolution · 2025Article
- Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities.PLoS computational biology · 2025Article
- PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models.Systematic biology · 2024Article
- ReMASTER: improved phylodynamic simulation for BEAST 2.7.Bioinformatics (Oxford, England) · 2024Article
- PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models.bioRxiv : the preprint server for biology · 2023Article
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4 authors.
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Abstract
Phylogenetic models have become increasingly complex, and phylogenetic data sets have expanded in both size and richness. However, current inference tools lack a model specification language that can concisely describe a complete phylogenetic analysis while remaining independent of implementation details. We introduce a new lightweight and concise model specification language, 'LPhy', which is designed to be both human and machine-readable. A graphical user interface accompanies 'LPhy', allowing users to build models, simulate data, and create natural language narratives describing the models. These narratives can serve as the foundation for manuscript method sections. Additionally, we present a command-line interface for converting LPhy-specified models into analysis specification files (in XML format) compatible with the BEAST2 software platform. Collectively, these tools aim to enhance the clarity of descriptions and reporting of probabilistic models in phylogenetic studies, ultimately promoting reproducibility of results.
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Registered trials
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