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GSR: Simulator - SimCopy
| Attribute | Value |
|---|---|
| Title | SimCopy |
| Short Description | An R package simulating the evolution of copy number profiles along a tree. |
| Long Description | SimCopy is an R package simulating the evolution of copy number profiles along a tree. It relies on the PhyloSim package for performing the simulations by encoding the genomic regions as sites in sequences and using modified processes acting on them. Please note, that the SimCopy simulations are restricted to a single chromosome. The genomes are encoded as a sequence of sites containing integers identifying genomic regions. Negative integers represent inverted genomic regions. SimCopy supports 1) deletion - deletes genomic regions, 2) duplication - duplicates genomic regions, 3) inversion - changes the orientation of the genomic regions by taking the opposite of the corresponding integer, 4) inverted duplication - duplicates genomic regions and flips their orientation and 5) translocation - translocates a stretch of genomic regions. |
| Version | 0.2 |
| Project Started | 2012 |
| Last Release | 10 years, 11 months ago |
| Homepage | http://bit.ly/simcopy |
| Citations | Roland F. Schwarz, Anne Trinh, Botond Sipos, James D. Brenton, Nick Goldman, and Florian Markowetz , Phylogenetic Quantification of Intra-tumour Heterogeneity, PLoS Comput Biol, 04-10-2014 |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 05-21-2019 (1789 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence (Copy number profiles), |
| Variations | Amino acid variation, Insertion and Deletion, Inversion and Rearrangement, Other (Copy number alterations), |
| Simulation Method | Phylogenetic, Other (Monte carlo simulation based on modifed phylosim objects and processes.), |
| Input | |
| Data Type | |
| File format | NEXUS, Phylip, Program Specific (Phylogenetic trees storead as ape objects.), |
| Output | |
| Data Type | |
| Sequencing Reads | Other (Haploid copy number profiles, simulated alignment of genomic regions.), |
| 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, Indels and Others, Heterogeneity among Sites (Supports rate heterogeneity through phylosim.), |
| Events Allowed | |
| Other | |
| Interface | Script-based, |
| Development | |
| Tested Platforms | Windows, Linux and Unix, |
| Language | R, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using SimCopy has been provided.
Please propose new citations if you are aware of publications that use this software.