INDELible: A Flexible Simulator of Biological Sequence Evolution

By W. Fletcher, Ziheng Yang. 2009

443 citations recorded by the source corpus.

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.

Subfields: Artificial Intelligence, Molecular Biology, Plant Science

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “For example, in a benchmark using simulated protein sequences (Lo¨ytynoja et al. 2012) generated by INDELiBLE (Fletcher and Yang 2009), when we tested a more stringent scoring matrix, JTT 1PAM (Jones et al. 1992) with weaker gap penalties than the default, the benchmark scores were considerably…”
A simple method to control over-alignment in the MAFFT multiple sequence alignment program (2016, methodology): “We used INDEliBLE version 1.03 (Fletcher and Yang, 2009) with the WAG model (Whelan and Goldman, 2001) for this simulation.”
Efficient ancestry and mutation simulation with msprime 1.0 (2021, background): “For example, we intend to add support for microsatellites (Mailund et al. 2005), codon models (Arenas and Posada 2007), and indels (Cartwright 2005; Fletcher and Yang 2009), although changes may be required to tskit ’s data model which is currently based on the assumption of independent sites.”
Renewing Felsenstein’s Phylogenetic Bootstrap in the Era of Big Data (2018, methodology): “Protein sequences were evolved along this tree using INDELible 49 , which was launched with options and parameter values derived from the PhyML analysis, and similar to the experiments conducted by Aberer et al. 24 to assess the accuracy of rogue-taxon detection: • Length of the root sequence: 250 A”
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters (2015, unknown): “Sequences were simulated using INDELible (35).”
Phylogenetic relationships of Santalales with insights into the origins of holoparasitic Balanophoraceae (2015, methodology): “The seven sets of trimmed tree topology, branch lengths and model parameter estimates were individually used to simulate 100 single-gene datasets in INDELible v.1.03 (Fletcher & Yang, 2009).”
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences (2015, methodology): “To explore performance on larger datasets, we simulated 10,000-sequence datasets using Indelible v. 1.03 (Fletcher and Yang, 2009) under three different rates of evolution (10 replicates each), with average sequence length 1000.”
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes (2015, methodology): “com/adamallo/SimPhy) to simulate species trees and gene trees (produced in mutation units) and then used Indelible (Fletcher and Yang, 2009) to simulate nucleotide sequences down the gene trees with varying length and model parameters. We estimated gene trees on these simulated gene alignments, whic”
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm (2012, methodology): “The alignment simulator INDELible (Fletcher and Yang, 2009) was used to generate codon sequences (see Supplementary Material for details) and the resulting data were analyzed both as DNA and protein.”
GUIDANCE: a web server for assessing alignment confidence scores (2010, methodology): “These studies included both simulated protein sequence benchmarks, using the simulators ROSE (7) and INDELible (8), and the widely-accepted real biological benchmark BAliBASE (9).”
Multiple Sequence Alignment (2005, background): “protein datasets and ModelTest [53] or PLTB [54] for nucleotide datasets).”
A general species delimitation method with applications to phylogenetic placements (2013, methodology): “We used ms (Hudson, 2002) and BioPerl (Stajich et al. , 2002) in combination with INDELible (Fletcher and Yang, 2009) to simulate sequences.”
An alignment confidence score capturing robustness to guide tree uncertainty. (2010, methodology): “Independent simulations of 100 data sets using the IN-DELible program (Fletcher and Yang 2009), which were not based on BAliBASE data, gave comparable results—an AUC of 90.1% for GUIDANCE and 88.4% for HoT.”
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference (2020, methodology): “03 [24] using parameters suggested by the software developers.”
IQ-TREE 3: phylogenomic inference software using complex evolutionary models (2026, unknown): “AliSim substantially outperforms Seq-Gen, Dawg, and INDELible in terms of both runtimes and memory usage.”
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees (2018, methodology): “We use Indelible [43] to simulate the nucleotide sequences along the gene trees using the GTR evolutionary model [44] with 4 different fixed sequence lengths: 1600, 800, 400, and 200bp.”