GSR: Simulator - SimCopy

Basic Package Attributes
AttributeValue
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 7 years, 5 months ago
Homepagehttp://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
Documentation
Application
Support

Last evaluated05-21-2019 (514 days ago)
Author verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence (Copy number profiles),
VariationsAmino acid variation, Insertion and Deletion, Inversion and Rearrangement, Other (Copy number alterations),
Simulation MethodPhylogenetic, Other (Monte carlo simulation based on modifed phylosim objects and processes.),
Input
Data Type
File formatNEXUS, Phylip, Program Specific (Phylogenetic trees storead as ape objects.),
Output
Data Type
Sequencing ReadsOther (Haploid copy number profiles, simulated alignment of genomic regions.),
File FormatFasta 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 ModelsMarkov DNA Evolution Models, Indels and Others, Heterogeneity among Sites (Supports rate heterogeneity through phylosim.),
Events Allowed
Other
InterfaceScript-based,
Development
Tested PlatformsWindows, Linux and Unix,
LanguageR,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation,

No example publication using SimCopy has been provided.

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