Evidence map›Paper›PMID 39847307›Full record

ArticleBulletin of mathematical biology2025

Bayesian Inference of Phylogenetic Distances: Revisiting the Eigenvalue Approach.

Matthew J Penn, Neil Scheidwasser, Christl A Donnelly, David A Duchêne, Samir Bhatt

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bulletin of mathematical biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Matthew J PennDepartment of Statistics, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0001-8682-5393
Neil ScheidwasserSection of Epidemiology, University of Copenhagen, Copenhagen, Denmark.
Christl A DonnellyDepartment of Statistics, University of Oxford, Oxford, UK.
David A DuchêneSection of Epidemiology, University of Copenhagen, Copenhagen, Denmark.
Samir BhattSection of Epidemiology, University of Copenhagen, Copenhagen, Denmark. bhattsamir@gmail.com.

Funding

Danish National Research Foundation DNRF160Engineering and Physical Sciences Research Council DTP Studentship (University of Oxford)European Research Council Marie Sklodowska-Curie fellowship H2020-MSCA-IF-2019-883832MRC Centre for Global Infectious Disease Analysis MR/X020258/1National Institute for Health and Care Research (NIHR) Health Protection Research Unit in Modelling and Health Economics NIHR200908NIHR HPRU in Emerging and Zoonotic Infections NIHR200907Novo Nordisk Fonden NNF20OC0059309Pioneer Centre for AI P1Schmidt Family Foundation G-22-63345
6 · The paper itself

Abstract

Using genetic data to infer evolutionary distances between molecular sequence pairs based on a Markov substitution model is a common procedure in phylogenetics, in particular for selecting a good starting tree to improve upon. Many evolutionary patterns can be accurately modelled using substitution models that are available in closed form, including the popular general time reversible model (GTR) for DNA data. For more complex biological phenomena, such as variations in lineage-specific evolutionary rates over time (heterotachy), other approaches such as the GTR with rate variation (GTR

Indexed as

Models, GeneticPhylogenyBayes TheoremComputer SimulationEvolution, MolecularMarkov ChainsMathematical ConceptsMonte Carlo MethodBayesian inferenceGenetic distanceGTRUkaryotes

Identifiers

PMID39847307
PMCPMC11759294

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Registered trials

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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.