ArticleMolecular biology and evolution2013
Bayesian selection of nucleotide substitution models and their site assignments.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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.
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.
Who cites it
23 citing papers in PubMed.
- Practical Guide and Review of Fossil Tip-Dating in Phylogenetics.Systematic biology · 2026Review
- Article
- Comparative analysis of complete mitochondrial genomes of fourteen moray eels (Anguilliformes: Muraenidae) and primary exploration of their phylogenetic relationship and temperature adaptation.BMC ecology and evolution · 2025Article
- Article
- The Primate Major Histocompatibility Complex: A Case Study of Gene Family Evolution.bioRxiv : the preprint server for biology · 2025Article
- Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation.Molecular biology and evolution · 2025Article
- Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation.Systematic biology · 2024Article
- Article
- BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.PLoS computational biology · 2019Article
- Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls.Frontiers in microbiology · 2019Review
- Information Criteria for Comparing Partition Schemes.Systematic biology · 2018Article
- Evolutionary dynamics of language systems.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- bModelTest: Bayesian phylogenetic site model averaging and model comparison.BMC evolutionary biology · 2017Article
- Insights into intercontinental spread of Zika virus.PloS one · 2017Article
- Analysis of Evolutionary Processes of Species Jump in Waterfowl Parvovirus.Frontiers in microbiology · 2017Article
- Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates.BMC evolutionary biology · 2015Article
- A simulation approach for change-points on phylogenetic trees.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
- An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs.Molecular biology and evolution · 2014Article
- An experimentally determined evolutionary model dramatically improves phylogenetic fit.Molecular biology and evolution · 2014Article
- Selecting optimal partitioning schemes for phylogenomic datasets.BMC evolutionary biology · 2014Article
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
Probabilistic inference of a phylogenetic tree from molecular sequence data is predicated on a substitution model describing the relative rates of change between character states along the tree for each site in the multiple sequence alignment. Commonly, one assumes that the substitution model is homogeneous across sites within large partitions of the alignment, assigns these partitions a priori, and then fixes their underlying substitution model to the best-fitting model from a hierarchy of named models. Here, we introduce an automatic model selection and model averaging approach within a Bayesian framework that simultaneously estimates the number of partitions, the assignment of sites to partitions, the substitution model for each partition, and the uncertainty in these selections. This new approach is implemented as an add-on to the BEAST 2 software platform. We find that this approach dramatically improves the fit of the nucleotide substitution model compared with existing approaches, and we show, using a number of example data sets, that as many as nine partitions are required to explain the heterogeneity in nucleotide substitution process across sites in a single gene analysis. In some instances, this improved modeling of the substitution process can have a measurable effect on downstream inference, including the estimated phylogeny, relative divergence times, and effective population size histories.
Indexed as
Identifiers
What OpenQuestion holds
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.