GSR: Simulator - TreesimJ

Basic Package Attributes
AttributeValue
Title TreesimJ
Short Description A flexible, forward-time population genetic simulator
Long Description TreesimJ is a forward-time simulator of an evolving population that tracks the evolutionary tree of the entire population. The application offers an intuitive GUI, a variety of pre-configured models of fitness, mutation, and demography, and a suite of data collectors that analyze the population and emit data to one or more sources. To the user, TreesimJ offers a simple, easy to use interface, a variety of interchangeable 'models' describing many aspects of the evolving population, and many ways to quantify and summarize the state of the population. Since the entire tree of the population is tracked, TreesimJ can easily be used to asses the average time to most recent common ancestor, the level of tree imbalance, or the mean pairwise coalescent time. It can also compute a number of familiar population genetic statistics, such as the nucleotide diversity and the number of segregating sites (if a model of fitness that includes DNA is used). The list of potential data collecting items is long, and getting
Version 0.7
Project Started 2010
Last Release 10 years, 7 months ago
Homepagehttp://code.google.com/p/treesimj/
Citations O'Fallon B, TreesimJ: a flexible, forward time population genetic simulator., Bioinformatics, 09-01-2010 [ Abstract, cited in PMC ]
GSR Certification

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Application
Support

Last evaluated11-05-2020 (1 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 DataDiploid DNA Sequence,
VariationsBiallelic Marker, Single Nucleotide Variation,
Simulation MethodForward-time,
Input
Data Type
File formatXML,
Output
Data TypeGenotype or Sequence, Individual Relationship, Diversity Measures,
Sequencing ReadsOther (Tree depth, skewness or the mean time for two individuals to first share a common ancestor),
File FormatFasta or Fastq,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, User Defined,
Gene FlowUser-defined Matrix,
Spatiality
Life CycleDiscrete Generation Model,
Mating SystemRandom Mating,
FecundityConstant Number,
Natural Selection
DeterminantSingle-locus,
Models
Recombination
Mutation ModelsMarkov DNA Evolution Models,
Events AllowedPopulation Merge and Split, Population Events,
Other
InterfaceCommand-line, Graphical User Interface,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix, Solaris,
LanguageJava,
LicenseGNU Public License (V2),
GSR CertificationAccessibility,

No example publication using TreesimJ has been provided.

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