GSR: Simulator - NEOGEN
The NEOGEN package is not yet public.
Attribute | Value |
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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 | 4 years, 10 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 |
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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.