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GSR: Simulator - NEOGEN
The NEOGEN package is not yet public.
| Attribute | Value |
|---|---|
| Title | NEOGEN |
| Short Description | A tool to predict genetic effective population size (Ne) for species with generational overlap and to assist empirical Ne study design |
| Long Description | NeOGen (genetic Ne for Overlapping Generations analysis; pronounced Neo-gen) is point-&-click genetic effective population size (Ne) and demographic modelling software. The software, initially designed for sharks, is applicable to many overlapping-generation species with moderate to low population sizes and fecundity (such as mammals). NeOGen provides a cohesive linkage disequilibrium genetic Ne estimate (Ne.LD) analysis and population simulation framework that simulates both the demography and genetic composition of a population, given a small subset of fundamental species-specific life-history, demographic and genetic priors. NeOGen then guides the researchers in-silico to establish a tractable sampling regime, resulting in the numbers of samples and loci required to give accurate and precise Ne.LD estimates when empirical sampling is performed in the field. |
| Version | 1.3.0.6a1 |
| Project Started | 2018 |
| Last Release | 6 years, 8 months ago |
| Homepage | http://www.molecularfisherieslaboratory.com.au/neogen-v1-3-0-6-a1-software/ |
| Citations |
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| GSR Certification | This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification. |
| 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 | Genotype at Genetic Markers, Diploid DNA Sequence, |
| Variations | Biallelic Marker, Microsatellite, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | Allele Frequencies, |
| File format | Arlequin, Genepop, |
| Output | |
| Data Type | |
| Sequencing Reads | Other, |
| File Format | Other, |
| Sample Type | Random or Independent, |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined, |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | Varying Demographic Features, |
| Other | |
| Interface | Command-line, Graphical User Interface, |
| Development | |
| Tested Platforms | Windows, |
| Language | Python, |
| License | GNU Public License, |
| GSR Certification |
Number of Primary Citations: 2
Number of Non-Primary Citations: 0
No example publication using NEOGEN has been provided.
Please propose new citations if you are aware of publications that use this software.