ArticlePLoS computational biology2016
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 388 papers.
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Who cites it
388 citing papers in PubMed.
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- Evidence standards for multi-ancestry polygenic prediction.Genome biology · 2026Review
- On the use of generative models for demographic inference in malaria vectors from genomic data.G3 (Bethesda, Md.) · 2026Article
- ARGscape: a modular, interactive tool for manipulation of spatiotemporal ancestral recombination graphs.Bioinformatics (Oxford, England) · 2026Article
- Genomic Data Describe Population Structure but Struggle to Estimate Directed Connectivity Networks.Molecular ecology resources · 2026Article
- Large-Scale Genomics Reveals Three-Source Ancestry and Layered Adaptation to High Altitude in Tibetan Chickens.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome.Nature ecology & evolution · 2026Article
- The Effects of Post-Divergence Gene Flow on Simultaneous Divergence Time Testing.Molecular ecology resources · 2026Article
328 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
A central challenge in the analysis of genetic variation is to provide realistic genome simulation across millions of samples. Present day coalescent simulations do not scale well, or use approximations that fail to capture important long-range linkage properties. Analysing the results of simulations also presents a substantial challenge, as current methods to store genealogies consume a great deal of space, are slow to parse and do not take advantage of shared structure in correlated trees. We solve these problems by introducing sparse trees and coalescence records as the key units of genealogical analysis. Using these tools, exact simulation of the coalescent with recombination for chromosome-sized regions over hundreds of thousands of samples is possible, and substantially faster than present-day approximate methods. We can also analyse the results orders of magnitude more quickly than with existing methods.
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