GSR: Simulator - msprime

Basic Package Attributes
AttributeValue
Title msprime
Short Description A fast and accurate coalescent simulator.
Long Description Msprime is a reimplementation of Hudson’s classical ms program for modern datasets.
Version 0.7.0
Project Started 2015
Last Release 1 year, 8 months ago
Homepagehttps://pypi.python.org/pypi/msprime
Citations Kelleher J, Etheridge AM, McVean G, Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes., PLoS Comput Biol, 05-01-2016 [ Abstract, cited in PMC ]
GSR CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated03-21-2019 (576 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated Data
VariationsBiallelic Marker, Single Nucleotide Variation,
Simulation MethodStandard Coalescent, Exact Coalescent,
Input
Data Type
File formatMS,
Output
Data TypeGenotype or Sequence, Mutation,
Sequencing Reads
File FormatMS,
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 FlowStepping Stone Models, Island Models, Continent-Island Models, Sex or Age-Specific Migration Rates, Influenced by Environmental Factors, Admixed Population, User-defined Matrix, Other,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationUniform, Varying Recombination Rates,
Mutation ModelsTwo-allele Mutation Model, Infinite-sites Model,
Events AllowedPopulation Merge and Split, Varying Demographic Features, Population Events,
Other
InterfaceCommand-line, Script-based,
Development
Tested PlatformsMac OS X, Linux and Unix, Solaris,
LanguageC or C++, Python,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application, Support,

The following 5 publications are selected examples of applications that used msprime.

2018

Browning SR, Browning BL, Zhou Y, Tucci S, Akey JM, Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture., Cell, 03-22-2018 [Abstract]

Malinsky M, Svardal H, Tyers AM, Miska EA, Genner MJ, Turner GF, Durbin R, Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow., Nat Ecol Evol, 12-01-2018 [Abstract]

2017

Martin AR, Gignoux CR, Walters RK, Wojcik GL, Neale BM, Gravel S, Daly MJ, Bustamante CD, Kenny EE, Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations., Am J Hum Genet, 04-06-2017 [Abstract]

Jouganous J, Long W, Ragsdale AP, Gravel S, Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation., Genetics, 07-01-2017 [Abstract]

2016

Field Y, Boyle EA, Telis N, Gao Z, Gaulton KJ, Golan D, Yengo L, Rocheleau G, Froguel P, McCarthy MI, et al., Detection of human adaptation during the past 2000 years., Science, 11-11-2016 [Abstract]


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