ArticleMolecular biology and evolution2014
Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Addressing convergence in the emerging era of structural phylogenetics.Frontiers in molecular biosciences · 2026Article
- Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses.Nature structural & molecular biology · 2025Article
- Recent advances in the inference of deep viral evolutionary history.Journal of virology · 2025Review
- Protein Structural Phylogenetics.Genome biology and evolution · 2025Review
- Article
- A scalable analytical approach from bacterial genomes to epidemiology.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy.Genome biology and evolution · 2020Article
- Structural Phylogenetics with Confidence.Molecular biology and evolution · 2020Article
- Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates.Evolutionary bioinformatics online · 2020Article
- Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States.Molecular biology and evolution · 2019Article
- Article
- Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction.Systematic biology · 2019Article
- The Enigmatic Origin of Papillomavirus Protein Domains.Viruses · 2017Article
- A Generative Angular Model of Protein Structure Evolution.Molecular biology and evolution · 2017Article
- Historian: accurate reconstruction of ancestral sequences and evolutionary rates.Bioinformatics (Oxford, England) · 2017Article
- Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.PLoS computational biology · 2016Article
- Inferring Indel Parameters using a Simulation-based Approach.Genome biology and evolution · 2015Article
- Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs.BMC bioinformatics · 2015Article
- Phylogeny of Echinoderm Hemoglobins.PloS one · 2015Article
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Authors and funding
5 authors.
Funding
Abstract
For sequences that are highly divergent, there is often insufficient information to infer accurate alignments, and phylogenetic uncertainty may be high. One way to address this issue is to make use of protein structural information, since structures generally diverge more slowly than sequences. In this work, we extend a recently developed stochastic model of pairwise structural evolution to multiple structures on a tree, analytically integrating over ancestral structures to permit efficient likelihood computations under the resulting joint sequence-structure model. We observe that the inclusion of structural information significantly reduces alignment and topology uncertainty, and reduces the number of topology and alignment errors in cases where the true trees and alignments are known. In some cases, the inclusion of structure results in changes to the consensus topology, indicating that structure may contain additional information beyond that which can be obtained from sequences. We use the model to investigate the order of divergence of cytoglobins, myoglobins, and hemoglobins and observe a stabilization of phylogenetic inference: although a sequence-based inference assigns significant posterior probability to several different topologies, the structural model strongly favors one of these over the others and is more robust to the choice of data set.
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