The DOI matches its Crossref record; 80 of the 80 references it cites were found in a registry or an index.
INDELible: A Flexible Simulator of Biological Sequence Evolution
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
(1993) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040023 · Cited by 11,229
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
Exact stochastic simulation of coupled chemical reactions
Gillespie, D. T. (1977) · The Journal of Physical Chemistry · doi:10.1021/j100540a008 · Cited by 10,136
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
The rapid generation of mutation data matrices from protein sequences
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Bioinformatics · doi:10.1093/bioinformatics/8.3.275 · Cited by 6,947
Amino acid substitution matrices from protein blocks.
Henikoff, S., & Henikoff, J. G. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.22.10915 · Cited by 6,218
PAML: a program package for phylogenetic analysis by maximum likelihood
Yang, Z. (1997) · Bioinformatics · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,373
Self-citation
Cited by
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
ModelFinder: fast model selection for accurate phylogenetic estimates
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017) · Nature Methods · doi:10.1038/nmeth.4285 · Cited by 18,449
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
Zhang, C., Rabiee, M., Sayyari, E., & Mirarab, S. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2129-y · Cited by 2,471
Sela, I., Ashkenazy, H., Katoh, K., & Pupko, T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv318 · Cited by 835
Pease, J. B., Brown, J. W., Walker, J. F., Hinchliff, C. E., & Smith, S. A. (2018) · American Journal of Botany · doi:10.1002/ajb2.1016 · Cited by 341
Metadata
- Authors
- Fletcher, W., & Yang, Z.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-05-07
- Volume
- 26
- Issue
- 8
- Pages
- 1879-1888
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2157552136
- Cited by
- 423
- References
- 80
- FWCI
- 6.12
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: INDELible: A Flexible Simulator of Biological Sequence Evolution. https://app.cochat.ai/papers/10.1093/molbev/msp098
- The paper
- Fletcher, W., & Yang, Z. (2009). INDELible: A Flexible Simulator of Biological Sequence Evolution. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msp098
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
