ReviewNature ecology & evolution2017
A biologist's guide to Bayesian phylogenetic analysis.
Review in Nature ecology & evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 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
78 citing papers in PubMed.
- Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa.Viruses · 2022Trial
- Sydney Phylogenetics Workshop: Lessons From the Past 15 Years.Ecology and evolution · 2026Article
- A deep learning-based score to evaluate multiple sequence alignments.Molecular biology and evolution · 2026Article
- Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era.Biochemical genetics · 2026Review
- Resurrecting Full-Length Ancestral Schizorhodopsins and Heliorhodopsins with Structure-Guided, Indel-Aware Sequence Reconstruction.ACS omega · 2026Article
- Practical Guide and Review of Fossil Tip-Dating in Phylogenetics.Systematic biology · 2026Review
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Trophic niche partitioning in giant clams.Communications biology · 2025Article
- Recent horizontal transfer of transposable elements inbioRxiv : the preprint server for biology · 2025Article
- The origin, evolution, and diversification of MADS-box transcription factors in green plants.Plant communications · 2025Article
- Robust phylodynamic inference and model specification for HIV transmission dynamics.Epidemics · 2025Article
- Rethinking Hominin Air Sac Loss in Light of Phylogenetically Meaningful Evidence.Evolutionary anthropology · 2025Article
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.bioRxiv : the preprint server for biology · 2025Article
- Article
- Annotated Bioinformatic Pipelines for Phylogenomic Placement of Mitochondrial Genomes.Bio-protocol · 2025Article
- Phylogenetic meta-analysis of persistent SARS-CoV-2 infections in immunocompromised individuals highlights the challenges of robust evolutionary rate estimation caused by low genetic diversity.Virus evolution · 2025Article
- Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs.Bioinformatics advances · 2025Review
- Article
- Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies.Bioinformatics and biology insights · 2025Article
- Genomic Evidence for the Purging of Deleterious Genetic Variation in the Endangered North Atlantic Right Whale.Evolutionary applications · 2024Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. Here, we summarize the major features of Bayesian phylogenetic inference and discuss Bayesian computation using Markov chain Monte Carlo (MCMC), the diagnosis of an MCMC run, and ways of summarising the MCMC sample. We discuss the specification of the prior, the choice of the substitution model, and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software and provide recommendations as to their use.
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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.