This repo contains the manuscript for the publication describing the msprime 1.0 paper.
Coalescent simulation is a key tool in population genetics and and has been integral to coalescent theory since its earliest days. Because of the ease at which the basic model can be simulated, a large number of different simulators have been developed. However, the coalescent with recombination is far more challenging to simulate, and, until recently, it was not possible to simulate efficiently. The msprime software has revolutionised coalescent simulation, making it possible to simulate millions of whole genomes for the first time. We summarise the many features of msprime 1.0, which is built around a core model of efficiently implementing recombination via the succinct tree sequence data structure. We advocate a community oriented open-source development process as a way to reduce duplication of effort and increase the quality of simulation software.
Like the development of msprime itself, the process of writing this article is managed through an open source development model via GitHub. Those responsible for particular features will be assigned sections of writing via issues. Those wishing to make edits should also follow these guidelines:
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