ArticleVirus evolution2019
SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination.
Article in Virus evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- wavess 1.2: Presenting an HLA-aware within-host virus sequence simulation framework.bioRxiv : the preprint server for biology · 2026Article
- e3SIM: Epidemiological-ecological-evolutionary simulation framework for genomic epidemiology.Methods in ecology and evolution · 2026Article
- wavess 1.2: presenting an HLA-aware within-host virus sequence simulation framework.Bioinformatics advances · 2026Article
- Article
- wavess: An R package for simulation of adaptive within-host virus sequence evolution.PLoS computational biology · 2025Article
- VITALdb: to select the best viroinformatics tools for a desired virus or application.Briefings in bioinformatics · 2025Article
- ViralBottleneck: an R package for estimating viral transmission bottlenecks from deep sequencing data using multiple methods.Virus evolution · 2025Article
- Evolutionary trajectory estimation via replication simulation of coronavirus spike gene based on random mutation and similarity-based selection.Computational and structural biotechnology journal · 2025Article
- Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.Viruses · 2024Article
- Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.bioRxiv : the preprint server for biology · 2024Article
- Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.Virus evolution · 2024Article
- Inferring Human Immunodeficiency Virus 1 Proviral Integration Dates With Bayesian Inference.Molecular biology and evolution · 2023Article
- A systems approach evaluating the impact of SARS-CoV-2 variant of concern mutations on CD8+ T cell responses.Immunotherapy advances · 2023Article
- Evaluation of recombination detection methods for viral sequencing.Virus evolution · 2023Article
- Genomic epidemiological models describe pathogen evolution across fitness valleys.Science advances · 2022Article
- Evolution during primary HIV infection does not require adaptive immune selection.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination.Genome biology and evolution · 2022Article
- Widespread interspecific phylogenetic tree incongruence between mosquito-borne and insect-specific flaviviruses at hotspots originally identified in Zika virus.Virus evolution · 2022Article
- A multi-task CNN learning model for taxonomic assignment of human viruses.BMC bioinformatics · 2021Article
- Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e.eLife · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Simulations are widely used to provide expectations and predictive distributions under known conditions against which to compare empirical data. Such simulations are also invaluable for testing and comparing the behaviour and power of inference methods. We describe SANTA-SIM, a software package to simulate the evolution of a population of gene sequences forwards through time. It models the underlying biological processes as discrete components: replication, recombination, point mutations, insertion-deletions, and selection under various fitness models and population size dynamics. The software is designed to be intuitive to work with for a wide range of users and executable in a cross-platform manner.
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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 Socratic graph.