ArticleMolecular biology and evolution2009
Problems and solutions for estimating indel rates and length distributions.
Article in Molecular biology and evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed.
- Efficient algorithms for simulating sequences along a phylogenetic tree.Bioinformatics (Oxford, England) · 2026Article
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- Statistical framework to determine indel-length distribution.Bioinformatics (Oxford, England) · 2024Article
- High-resolution mapping reveals the mechanism and contribution of genome insertions and deletions to RNA virus evolution.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Molecular Characterization and Genetic Diversity of Ginkgo (Plants (Basel, Switzerland) · 2023Article
- Development of Omni InDel and supporting database for maize.Frontiers in plant science · 2023Article
- 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
- AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era.Molecular biology and evolution · 2022Article
- A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions.Molecular biology and evolution · 2021Article
- Short-range template switching in great ape genomes explored using pair hidden Markov models.PLoS genetics · 2021Article
- The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment.Systematic biology · 2021Article
- PGsim: A Comprehensive and Highly Customizable Personal Genome Simulator.Frontiers in bioengineering and biotechnology · 2020Article
- Exome sequencing in genomic regions related to racing performance of Quarter Horses.Journal of applied genetics · 2019Article
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- Correlated Selection on Amino Acid Deletion and Replacement in Mammalian Protein Sequences.Journal of molecular evolution · 2018Article
- Patterns of Nucleotide Deletion and Insertion Inferred from Bacterial Pseudogenes.Genome biology and evolution · 2018Article
- Alignment Modulates Ancestral Sequence Reconstruction Accuracy.Molecular biology and evolution · 2018Article
- The architecture of an empirical genotype-phenotype map.Evolution; international journal of organic evolution · 2018Article
- Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm.Bioinformatics (Oxford, England) · 2018Article
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Abstract
Insertions and deletions (indels) are fundamental but understudied components of molecular evolution. Here we present an expectation-maximization algorithm built on a pair hidden Markov model that is able to properly handle indels in neutrally evolving DNA sequences. From a data set of orthologous introns, we estimate relative rates and length distributions of indels among primates and rodents. This technique has the advantage of potentially handling large genomic data sets. We find that a zeta power-law model of indel lengths provides a much better fit than the traditional geometric model and that indel processes are conserved between our taxa. The estimated relative rates are about 12-16 indels per 100 substitutions, and the estimated power-law magnitudes are about 1.6-1.7. More significantly, we find that using the traditional geometric/affine model of indel lengths introduces artifacts into evolutionary analysis, casting doubt on studies of the evolution and diversity of indel formation using traditional models and invalidating measures of species divergence that include indel lengths.
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