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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 | 15 years, 2 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, Aug. 1, 2009 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | May 15, 2023 (705 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, June 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, Aug. 3, 2023 [Abstract]