GSR: Simulator - msprime
Attribute | Value |
---|---|
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 | 5 years, 2 months ago |
Homepage | https://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 Certification | ✔ Accessibility |
Last evaluated | 03-21-2019 (1850 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | |
Variations | Biallelic Marker, Single Nucleotide Variation, |
Simulation Method | Standard Coalescent, Exact Coalescent, |
Input | |
Data Type | |
File format | MS, |
Output | |
Data Type | Genotype or Sequence, Mutation, |
Sequencing Reads | |
File Format | MS, |
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 | Stepping 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 System | Random Mating, |
Fecundity | |
Natural Selection | |
Determinant | |
Models | |
Recombination | Uniform, Varying Recombination Rates, |
Mutation Models | Two-allele Mutation Model, Infinite-sites Model, |
Events Allowed | Population Merge and Split, Varying Demographic Features, Population Events, |
Other | |
Interface | Command-line, Script-based, |
Development | |
Tested Platforms | Mac OS X, Linux and Unix, Solaris, |
Language | C or C++, Python, |
License | GNU Public License, |
GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 5
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]