ArticleMolecular biology and evolution2021
A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- A deep learning-based score to evaluate multiple sequence alignments.Molecular biology and evolution · 2026Article
- Efficient algorithms for simulating sequences along a phylogenetic tree.Bioinformatics (Oxford, England) · 2026Article
- Performance assessment of phylogenetic inference tools using PhyloSmew.Bioinformatics advances · 2025Article
- BetaAlign: a deep learning approach for multiple sequence alignment.Bioinformatics (Oxford, England) · 2024Article
- Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction.BMC bioinformatics · 2024Article
- 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
- Article
- Effect of tokenization on transformers for biological sequences.Bioinformatics (Oxford, England) · 2024Article
- Statistical framework to determine indel-length distribution.Bioinformatics (Oxford, England) · 2024Article
- De Novo Structural Variations of Escherichia coli Detected by Nanopore Long-Read Sequencing.Genome biology and evolution · 2023Article
- The Telomeric Repeats of HHV-6A Do Not Determine the Chromosome into Which the Virus Is Integrated.Genes · 2023Article
- Development of Omni InDel and supporting database for maize.Frontiers in plant science · 2023Article
- Analysis of Copy Number Variation in the Whole Genome of Normal-Haired and Long-Haired Tianzhu White Yaks.Genes · 2022Article
- The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns.Open biology · 2022Article
- An Approximate Bayesian Computation Approach for Modeling Genome Rearrangements.Molecular biology and evolution · 2022Article
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11 authors.
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Abstract
Insertions and deletions (indels) are common molecular evolutionary events. However, probabilistic models for indel evolution are under-developed due to their computational complexity. Here, we introduce several improvements to indel modeling: 1) While previous models for indel evolution assumed that the rates and length distributions of insertions and deletions are equal, here we propose a richer model that explicitly distinguishes between the two; 2) we introduce numerous summary statistics that allow approximate Bayesian computation-based parameter estimation; 3) we develop a method to correct for biases introduced by alignment programs, when inferring indel parameters from empirical data sets; and 4) using a model-selection scheme, we test whether the richer model better fits biological data compared with the simpler model. Our analyses suggest that both our inference scheme and the model-selection procedure achieve high accuracy on simulated data. We further demonstrate that our proposed richer model better fits a large number of empirical data sets and that, for the majority of these data sets, the deletion rate is higher than the insertion rate.
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