ArticlePeerJ2020
OBAMA: OBAMA for Bayesian amino-acid model averaging.
Article in PeerJ, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Evolution, Mechanisms, and Therapeutic Implications of Mobile Tetracycline Destructases.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Collagen fingerprinting and sequence analysis provides a molecular phylogeny of extinct Australian megafauna.Proceedings. Biological sciences · 2025Article
- Article
- Mechanistic and evolutionary insights into a family of aminoacyl-tRNA deacylases that protects against canavanine toxicity.Nucleic acids research · 2025Article
- Reduced Amino Acid Substitution Matrices Find Traces of Ancient Coding Alphabets in Modern Day Proteins.Molecular biology and evolution · 2025Article
- Host-Calibrated Time Tree Caps the Age of Giant Viruses.Molecular biology and evolution · 2025Article
- AARS Online: A collaborative database on the structure, function, and evolution of the aminoacyl-tRNA synthetases.IUBMB life · 2024Article
- An independent base composition of each rate class for improved likelihood-based phylogeny estimation; the 5rf model.bioRxiv : the preprint server for biology · 2024Article
- Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage.Nature communications · 2024Article
- Enzymic recognition of amino acids drove the evolution of primordial genetic codes.Nucleic acids research · 2024Article
- Consequences of Genetic Recombination on Protein Folding Stability.Journal of molecular evolution · 2023Article
- An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference.Systematic biology · 2022Article
- StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent.Systematic biology · 2022Article
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1 author.
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Abstract
backgroundBayesian analyses offer many benefits for phylogenetic, and have been popular for analysis of amino acid alignments. It is necessary to specify a substitution and site model for such analyses, and often an ad hoc, or likelihood based method is employed for choosing these models that are typically of no interest to the analysis overall.
methodsWe present a method called OBAMA that averages over substitution models and site models, thus letting the data inform model choices and taking model uncertainty into account. It uses trans-dimensional Markov Chain Monte Carlo (MCMC) proposals to switch between various empirical substitution models for amino acids such as Dayhoff, WAG, and JTT. Furthermore, it switches base frequencies from these substitution models or use base frequencies estimated based on the alignment. Finally, it switches between using gamma rate heterogeneity or not, and between using a proportion of invariable sites or not.
resultsWe show that the model performs well in a simulation study. By using appropriate priors, we demonstrate both proportion of invariable sites and the shape parameter for gamma rate heterogeneity can be estimated. The OBAMA method allows taking in account model uncertainty, thus reducing bias in phylogenetic estimates. The method is implemented in the OBAMA package in BEAST 2, which is open source licensed under LGPL and allows joint tree inference under a wide range of models.
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