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GSR: Simulator - Indelible
| Attribute | Value |
|---|---|
| Title | Indelible |
| Short Description | A powerful and flexible simulator of biological evolution |
| Long Description | INDELible is a new, portable, and flexible application for biological sequence simulation that combines many features in the same place for the first time. Using a length-dependent model of indel formation it can simulate evolution of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. |
| Version | 1.0.3 |
| Project Started | 2009 |
| Last Release | 13 years, 11 months ago |
| Homepage | http://abacus.gene.ucl.ac.uk/software/indelible/ |
| Citations | Fletcher W, Yang Z, INDELible: a flexible simulator of biological sequence evolution., Mol Biol Evol, 08-01-2009 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 05-15-2023 (334 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, Protein Sequence, |
| Variations | Biallelic Marker, Amino acid variation, Insertion and Deletion, |
| Simulation Method | Phylogenetic, |
| Input | |
| Data Type | Ancestral Sequence, |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | Fasta or Fastq, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites, |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used Indelible.
2023
Leal JL, Milesi P, Salojärvi J, Lascoux M, Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences., Syst Biol, 06-16-2023 [Abstract]
Olabode AS, Mumby MJ, Wild TA, Muñoz-Baena L, Dikeakos JD, Poon AFY, Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses., Mol Biol Evol, 08-03-2023 [Abstract]