ArticleGenetics2022
Efficient ancestry and mutation simulation with msprime 1.0.
Article in Genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 315 papers.
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315 citing papers in PubMed.
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- Gene tree patterns help answer: vicariance or dispersal?bioRxiv : the preprint server for biology · 2026Article
- COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs.Genome biology · 2026Article
- Genomic Evidence of Early-Diverging Domesticated Lineages in Norwegian Farmhouse Yeast.Genome biology and evolution · 2026Article
- Comparing ARG Inference Methods Under Transmission of Reproductive Success: Tree Imbalance Matters.Genome biology and evolution · 2026Article
- Phylogenetically Diverse Introgression Drives Subtle Population Structure in Pacific Rockfishes.Molecular ecology · 2026Article
- Population genomics reveals multi-scale mechanisms sustaining schistosomiasis re-emergence in a near-elimination setting.PLoS neglected tropical diseases · 2026Article
- High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV.Genome research · 2026Article
- Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data.Molecular biology and evolution · 2026Article
- The dynamics of introgression and parallel adaptation across North AmericanProceedings of the National Academy of Sciences of the United States of America · 2026Article
- diempy: fast and reference-free genome polarization and chromosome painting.G3 (Bethesda, Md.) · 2026Article
- Faster inference of complex demographic models from large allele frequency spectra.Bioinformatics (Oxford, England) · 2026Article
- Biobank-scale genotype similarity search and dynamic patient-matched cohort creation with GenoSiS.Genome research · 2026Article
- Maintenance of phenotypic divergence in two sympatric monkeyflowers with weak reproductive isolation.bioRxiv : the preprint server for biology · 2026Article
- Improving Malaria Parasite Gene Flow Inference Under Sparse Spatial Sampling.Molecular ecology resources · 2026Article
- The rights and wrongs of rescaling in population genetics simulations.PLoS genetics · 2026Review
- Updating the RZooRoH Package for the Analysis of Inbreeding, Identity-By-Descent and Relatedness From Genomic Data.Molecular ecology resources · 2026Article
- Rapid expansion overcomes inbreeding in cross-hemisphere colonization of Barn Swallows.bioRxiv : the preprint server for biology · 2026Article
255 more citing papers are in PubMed but not listed here.
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Authors and funding
32 authors.
Funding
Abstract
Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and the tskit library. We summarize msprime's many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.