msprime statistics

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msprime specifications


Unique identifier OMICS_15319
Name msprime
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.4.0
Stability Stable
GNU Scientific, HDF5
Maintained Yes



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  • person_outline Jerome Kelleher <>

Publication for msprime

msprime in publications

PMCID: 5809101
PMID: 29385127
DOI: 10.1371/journal.pgen.1007191

[…] only populations 1 and 2 (that belong to a single side of the balanced tree) were represented in the panel., to evaluate the robustness of the model to ld, we simulated additional datasets using msprime [], because our generation-by-generation simulator is not designed to generate linked markers. considering a population history with balanced topology ((1,2),(3,4)), we generated 100 […]

PMCID: 5759368
PMID: 29310567
DOI: 10.1186/s12859-017-2002-4

[…] tasets, if the loci are even shorter, one can expect even better sensitivity of the d-statistic compared with our results. in the future, backward simulations based on coalescence algorithms, such as msprime [], can be employed to further pinpoint the effects of locus size and recombination rate., the d-statistic was developed to detect gene flow in both directions, i.e. h2 - > h3 and h3 - > […]

PMCID: 5850838
PMID: 29216397
DOI: 10.1093/molbev/msx300

[…] in ne(t) (). therefore, we examined specific features of our inference with a simulation scheme. we simulated genome-wide data under alternative demographic scenarios with the coalescence simulator msprime (), and inferred ne(t) on the simulated data using msmc. we then compared the ne(t) estimates from the simulated data sets to the one estimated from real data (see materials and methods […]

PMCID: 5753871
PMID: 29167200
DOI: 10.1534/genetics.117.300448

[…] at, to explore the tradeoff of sequencing more individuals at lower depth compared to fewer individuals at higher coverage, we performed simulations using msprime () combined with custom scripts to simulate error and low coverage data. briefly, we assumed a poisson distribution of reads at every site with mean given by the coverage, and then simulated […]

PMCID: 5578687
PMID: 28827797
DOI: 10.1371/journal.pgen.1006963

[…] discuss in the results section, resulted in good statistical properties of the method., we tested the performance of our method on simulated pedigrees. we generated human autosomal haplotypes using msprime [] with effective population size of 10,000, average recombination rate of 1.3e-8, and mutation rate of 1.25e-8. using these founder haplotypes, we simulated four pedigree structures shown […]

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msprime institution(s)
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Statistics, University of Oxford, Oxford, UK; Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
msprime funding source(s)
This work was supported by Wellcome Trust core award 090532/Z/09/Z to the Wellcome Trust Centre for Human Genetics, Wellcome Trust grant 100956/Z/13/Z, EPSRC grants EP/I01361X/1, EP/I013091/1 and EP/K034316/1.

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