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GSR: Simulator - REvolver
| Attribute | Value |
|---|---|
| Title | REvolver |
| Short Description | Modeling sequence evolution under domain constraints |
| Long Description | REvolver is a program to simulate protein sequence evolution. REvolver automatically integrates domain information described by a profile Hidden Markov Model (pHMM) into the simulation. In the simulation of protein evolution it often had been assumed that sites evolve identically and independently from each other. This simplification is necessary since information concerning site specific evolution is frequently unavailable. However, homologous sequences and domains have been collected, aligned, and pHMMs built. The pHMM describes the variability and shared characteristics of sequences that share a common ancestor. Here we do have knowledge about what sites are conserved, at what positions in the sequences insertions are more likely, or what sites can be deleted. Pfam (Finn et al., 2010) and SMART (Letunic, Doerks and Bork, 2009) are examples for databases providing such data. REvolver is the first method, for simulating protein sequence evolution that integrates this pre-existing information about evolution in an automatic fashion. |
| Last Release | 12 years, 8 months ago |
| Homepage | http://www.cibiv.at/software/revolver/ |
| Citations | Koestler T, von Haeseler A, Ebersberger I, REvolver: modeling sequence evolution under domain constraints., Mol Biol Evol, 09-01-2012 [ 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 | Protein Sequence, |
| Variations | Amino acid variation, |
| Simulation Method | Other, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | |
| 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 | |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | Java, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using REvolver has been provided.
Please propose new citations if you are aware of publications that use this software.