phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets Long Description (required)
We present phastSim, a new algorithm and software for efficiently simulating sequence evolution along extremely large trees (e.g. > 100, 000 tips) when the branches of the tree are short, as is typical in genomic epidemiology. Our algorithm is based on the Gillespie approach, and it implements an efficient multi-layered search tree structure that provides high computational efficiency by taking advantage of the fact that only a small proportion of the genome is likely to mutate at each branch of the considered phylogeny. Our open source software allows easy integration with other Python packages as well as a variety of evolutionary models, including indel models and new hypermutability models that we developed to more realistically represent SARS-CoV-2 genome evolution. large datasets, sequence evolution, genomic epidemiology, Gillespie algorithm, https://github.com/NicolaDM/phastSim
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Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 35486906 ],
De Maio N, Boulton W, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N ,
phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets. ,
PLoS Comput Biol ,
04-29-2022 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=35486906, Primary Citation
[Pubmed ID: 35611334 ],
Thornlow B, Kramer A, Ye C, De Maio N, McBroome J, Hinrichs AS, Lanfear R, Turakhia Y, Corbett-Detig R ,
Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than <i>de novo</i> and Maximum-Likelihood Approaches. ,
bioRxiv ,
05-18-2022 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=35611334, , Application
[Pubmed ID: 35769891 ],
McBroome J, Martin J, de Bernardi Schneider A, Turakhia Y, Corbett-Detig R ,
Identifying SARS-CoV-2 regional introductions and transmission clusters in real time. ,
Virus Evol ,
06-16-2022 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=35769891, , Application