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GSR: Simulator - Rose
| Attribute | Value |
|---|---|
| Title | Rose |
| Short Description | Random model of sequence evolution |
| Long Description | Rose implements a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary process, the `true' history is logged and the `correct' multiple sequence alignment is created simultaneously. The model also allows for varying rates of mutation within the sequences, making it possible to establish so-called sequence motifs. The data created by Rose are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships. It can also be useful when teaching courses in or developing models of sequence evolution and in the study of evolutionary processes. |
| Version | 1.3 |
| Project Started | 1998 |
| Last Release | 26 years, 1 month ago |
| Homepage | http://bibiserv.techfak.uni-bielefeld.de/rose/ |
| Citations | Stoye J, Evers D, Meyer F, Rose: generating sequence families., Bioinformatics, 01-01-1998 [ 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, RNA, Protein Sequence, |
| Variations | Insertion and Deletion, |
| Simulation Method | Phylogenetic, |
| Input | |
| Data Type | |
| File format | Program Specific, |
| Output | |
| Data Type | Genotype or Sequence, |
| 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 | Markov DNA Evolution Models, Indels and Others, |
| Events Allowed | |
| Other | |
| Interface | |
| Development | |
| Tested Platforms | Linux and Unix, Solaris, |
| Language | C or C++, |
| License | |
| GSR Certification | Accessibility, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used Rose.
2023
Park M, Warnow T, HMMerge: an ensemble method for multiple sequence alignment., Bioinform Adv, 04-17-2023 [Abstract]
2022
Lipták P, Kiss A, Szalai-Gindl JM, Heuristic Pairwise Alignment in Database Environments., Genes (Basel), 11-02-2022 [Abstract]