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GSR: Simulator - indel-Seq-Gen
| Attribute | Value |
|---|---|
| Title | indel-Seq-Gen |
| Short Description | A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies |
| Long Description | indel-Seq-Gen (iSG) is a biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies. This is accomplished through the addition of subsequence length constraints and lineage- and site-specific evolution. iSG tracks insertion and deletion processes that occur during the simulation run. iSG records all evolutionary events and outputs the "true" multiple alignment of the sequences, and can generate a larger simulated sequence space by allowing the use of multiple related root sequences. iSG can be used to test the accuracy of multiple alignment methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein superfamily classification methods. |
| Version | 2.1.03 |
| Project Started | 2010 |
| Last Release | 13 years, 3 months ago |
| Homepage | http://bioinfolab.unl.edu/~cstrope/iSG/ |
| Citations | Strope CL, Scott SD, Moriyama EN, indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels., Mol Biol Evol, 03-01-2007 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 10-15-2020 (1276 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 | Amino acid variation, Insertion and Deletion, |
| Simulation Method | Phylogenetic, |
| Input | |
| Data Type | Ancestral Sequence, |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship, |
| 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 | Markov DNA Evolution Models, Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites, |
| Events Allowed | |
| Other | |
| Interface | Command-line, Graphical User Interface (Through suitemsa (http://bioinfolab.unl.edu/~canderson/suitemsa/) ), |
| Development | |
| Tested Platforms | Windows (Mingw), 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 indel-Seq-Gen.
2020
Aadland K, Kolaczkowski B, Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy., Genome Biol Evol, 09-01-2020 [Abstract]
Dai H, Guan Y, The Nubeam reference-free approach to analyze metagenomic sequencing reads., Genome Res, 09-01-2020 [Abstract]