ArticleMolecular biology and evolution2009
INDELible: a flexible simulator of biological sequence evolution.
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 226 papers.
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226 citing papers in PubMed.
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- A deep learning-based score to evaluate multiple sequence alignments.Molecular biology and evolution · 2026Article
- CAMUS: scalable phylogenetic network estimation.Bioinformatics (Oxford, England) · 2026Article
- Incorporating indel channels into average-case analysis of seed-chain-extend.Bioinformatics (Oxford, England) · 2026Article
- Selection profiles in RNA viruses reflect the characteristics of viruses more than individual proteins.PLoS pathogens · 2026Article
- IQ-TREE 3: phylogenomic inference software using complex evolutionary models.Molecular biology and evolution · 2026Article
- WASTER: Practical de novo Phylogenomics from Low-coverage Short Reads.Molecular biology and evolution · 2026Article
- Deep models of protein evolution in time generate realistic evolutionary trajectories and functional proteins.bioRxiv : the preprint server for biology · 2026Article
- Efficient algorithms for simulating sequences along a phylogenetic tree.Bioinformatics (Oxford, England) · 2026Article
- Impact of Data Error on Phylogenetic Network Inference from Gene Trees Under the Multispecies Network Coalescent.Methods in molecular biology (Clifton, N.J.) · 2026Article
- HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes.Genome biology · 2025Article
- Phylogenetic Methods Meet Deep Learning.Genome biology and evolution · 2025Article
- Detecting Interspecific Positive Selection Using Convolutional Neural Networks.Molecular biology and evolution · 2025Article
- Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes.Genome research · 2025Article
- Unraveling myriapod evolution: sealion, a novel quartet-based approach for evaluating phylogenetic uncertainty.NAR genomics and bioinformatics · 2025Article
- Performance assessment of phylogenetic inference tools using PhyloSmew.Bioinformatics advances · 2025Article
- Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction.BMC bioinformatics · 2024Article
- ReAlign-N: an integrated realignment approach for multiple nucleic acid sequence alignment, combining global and local realignments.NAR genomics and bioinformatics · 2024Article
- HAlign 4: a new strategy for rapidly aligning millions of sequences.Bioinformatics (Oxford, England) · 2024Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
166 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Many methods exist for reconstructing phylogenies from molecular sequence data, but few phylogenies are known and can be used to check their efficacy. Simulation remains the most important approach to testing the accuracy and robustness of phylogenetic inference methods. However, current simulation programs are limited, especially concerning realistic models for simulating insertions and deletions. We implement a portable and flexible application, named INDELible, for generating nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. Indels are simulated under several models of indel-length distribution. The program implements a rich repertoire of substitution models, including the general unrestricted model and nonstationary nonhomogeneous models of nucleotide substitution, mixture, and partition models that account for heterogeneity among sites, and codon models that allow the nonsynonymous/synonymous substitution rate ratio to vary among sites and branches. With its many unique features, INDELible should be useful for evaluating the performance of many inference methods, including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or genome reconstruction.
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