GSR: Simulator - NEOGEN

The NEOGEN package is not yet public.

Basic Package Attributes
AttributeValue
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
Homepagehttp://www.molecularfisherieslaboratory.com.au/neogen-v1-3-0-6-a1-software/
Citations
  • Blower DC, Riginos C, Ovenden JR, NeOGen: a tool to predict genetic effective population size (Ne) for species with generational overlap and to assist empirical Ne study design, Molecular Ecology Resources 19, 260-271., 08-28-2019 [ Abstract ]
  • Blower DC, Riginos C, Ovenden JR, neogen: A tool to predict genetic effective population size (N<sub>e</sub> ) for species with generational overlap and to assist empirical N<sub>e</sub> study design., Mol Ecol Resour, 01-01-2019 [ Abstract , cited in PMC ]
GSR Certification This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification.
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 DataGenotype at Genetic Markers, Diploid DNA Sequence,
VariationsBiallelic Marker, Microsatellite,
Simulation MethodForward-time,
Input
Data TypeAllele Frequencies,
File formatArlequin, Genepop,
Output
Data Type
Sequencing ReadsOther,
File FormatOther,
Sample TypeRandom or Independent,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant 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 AllowedVarying Demographic Features,
Other
InterfaceCommand-line, Graphical User Interface,
Development
Tested PlatformsWindows,
LanguagePython,
LicenseGNU Public License,
GSR Certification

Number of Primary Citations: 2

Number of Non-Primary Citations: 0

No example publication using NEOGEN has been provided.

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