Fast, whole-genome simulation of the discrete time Wright-Fisher process Long Description (required)
ARGON simulates the discrete time Wright Fisher process (DTWF) backwards in time. The coalescent is equivalent to the DTWF process if the sample size is small compared to the effective population size, but will deviate from it as the sample size increases (Wakeley and Takahashi, MBE 2003; Bhaskar, Clark and Song, PNAS 2014). ARGON supports arbitrary demographic history, migration, variable mutation/recombination rates and gene conversion, and efficiently outputs pairwise identical-by-descent (IBD) sharing data. https://github.com/pierpal/ARGON
Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.
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Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s).
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Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 27312410 ],
Palamara PF ,
ARGON: fast, whole-genome simulation of the discrete time Wright-fisher process. ,
Bioinformatics ,
10-01-2016 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=27312410, Primary Citation
[Pubmed ID: 34595352 ],
Fitak RR ,
OptM: estimating the optimal number of migration edges on population trees using Treemix. ,
Biol Methods Protoc ,
09-16-2021 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=34595352, , Application
[Pubmed ID: 34897427 ],
Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman EC, Galloway JG, et al. ,
Efficient ancestry and mutation simulation with msprime 1.0. ,
Genetics ,
03-03-2022 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=34897427, , Application