GSR: Simulator - TreesimJ
Attribute | Value |
---|---|
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 | 13 years, 10 months ago |
Homepage | http://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 | ✔ Accessibility |
Last evaluated | 11-05-2020 (1234 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 | Diploid DNA Sequence, |
Variations | Biallelic Marker, Single Nucleotide Variation, |
Simulation Method | Forward-time, |
Input | |
Data Type | |
File format | XML, |
Output | |
Data Type | Genotype or Sequence, Individual Relationship, Diversity Measures, |
Sequencing Reads | Other (Tree depth, skewness or the mean time for two individuals to first share a common ancestor), |
File Format | Fasta or Fastq, |
Sample Type | |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Constant Size, Exponential Growth or Decline, User Defined, |
Gene Flow | User-defined Matrix, |
Spatiality | |
Life Cycle | Discrete Generation Model, |
Mating System | Random Mating, |
Fecundity | Constant Number, |
Natural Selection | |
Determinant | Single-locus, |
Models | |
Recombination | |
Mutation Models | Markov DNA Evolution Models, |
Events Allowed | Population Merge and Split, Population Events, |
Other | |
Interface | Command-line, Graphical User Interface, |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, Solaris, |
Language | Java, |
License | GNU Public License (V2), |
GSR Certification | Accessibility, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using TreesimJ has been provided.
Please propose new citations if you are aware of publications that use this software.