ArticlePLoS computational biology2022
phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.Nature methods · 2026Article
- Rate variation and recurrent sequence errors in pandemic-scale phylogenetics.Nature methods · 2026Article
- RECUR: identifying recurrent amino acid substitutions from multiple sequence alignments.Molecular biology and evolution · 2026Article
- Efficient algorithms for simulating sequences along a phylogenetic tree.Bioinformatics (Oxford, England) · 2026Article
- Article
- Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA).Molecular biology and evolution · 2025Article
- SNiPgenie: a tool for microbial SNP site detection from whole-genome sequencing data.Access microbiology · 2025Article
- Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.bioRxiv : the preprint server for biology · 2024Article
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations.Systematic biology · 2023Article
- AliSim-HPC: parallel sequence simulator for phylogenetics.Bioinformatics (Oxford, England) · 2023Article
- Maximum likelihood pandemic-scale phylogenetics.Nature genetics · 2023Article
- Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- VGsim: Scalable viral genealogy simulator for global pandemic.PLoS computational biology · 2022Article
- Maximum likelihood pandemic-scale phylogenetics.bioRxiv : the preprint server for biology · 2022Article
- Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies thanbioRxiv : the preprint server for biology · 2022Article
- AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era.Molecular biology and evolution · 2022Article
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
- Identifying SARS-CoV-2 regional introductions and transmission clusters in real time.Virus evolution · 2022Article
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7 authors.
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Abstract
Sequence simulators are fundamental tools in bioinformatics, as they allow us to test data processing and inference tools, and are an essential component of some inference methods. The ongoing surge in available sequence data is however testing the limits of our bioinformatics software. One example is the large number of SARS-CoV-2 genomes available, which are beyond the processing power of many methods, and simulating such large datasets is also proving difficult. Here, we present 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.
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Registered trials
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.