ArticleBMC evolutionary biology2007
Incorporating indel information into phylogeny estimation for rapidly emerging pathogens.
Article in BMC evolutionary biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed.
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- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Reliable estimation of tree branch lengths using deep neural networks.PLoS computational biology · 2024Article
- COATi: Statistical Pairwise Alignment of Protein-Coding Sequences.Molecular biology and evolution · 2024Article
- Evaluation of various distance computation methods for construction of haplotype-based phylogenies from large MLST datasets.Molecular phylogenetics and evolution · 2022Article
- Correlations between alignment gaps and nucleotide substitution or amino acid replacement.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Machine Boss: rapid prototyping of bioinformatic automata.Bioinformatics (Oxford, England) · 2021Article
- Indels in SARS-CoV-2 occur at template-switching hotspots.BioData mining · 2021Article
- The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment.Systematic biology · 2021Article
- Revisiting Evaluation of Multiple Sequence Alignment Methods.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP.Methods in molecular biology (Clifton, N.J.) · 2021Article
- The GH19 Engineering Database: Sequence diversity, substrate scope, and evolution in glycoside hydrolase family 19.PloS one · 2021Article
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- Endolysins from AntarcticMarine drugs · 2020Article
- Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy.Genome biology and evolution · 2020Article
- Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny.BMC plant biology · 2019Article
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2 authors.
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Abstract
backgroundPhylogenies of rapidly evolving pathogens can be difficult to resolve because of the small number of substitutions that accumulate in the short times since divergence. To improve resolution of such phylogenies we propose using insertion and deletion (indel) information in addition to substitution information. We accomplish this through joint estimation of alignment and phylogeny in a Bayesian framework, drawing inference using Markov chain Monte Carlo. Joint estimation of alignment and phylogeny sidesteps biases that stem from conditioning on a single alignment by taking into account the ensemble of near-optimal alignments.
resultsWe introduce a novel Markov chain transition kernel that improves computational efficiency by proposing non-local topology rearrangements and by block sampling alignment and topology parameters. In addition, we extend our previous indel model to increase biological realism by placing indels preferentially on longer branches. We demonstrate the ability of indel information to increase phylogenetic resolution in examples drawn from within-host viral sequence samples. We also demonstrate the importance of taking alignment uncertainty into account when using such information. Finally, we show that codon-based substitution models can significantly affect alignment quality and phylogenetic inference by unrealistically forcing indels to begin and end between codons.
conclusionThese results indicate that indel information can improve phylogenetic resolution of recently diverged pathogens and that alignment uncertainty should be considered in such analyses.
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