ArticleBioinformatics (Oxford, England)2015
SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 papers.
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118 citing papers in PubMed.
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- Ancient but dynamic: structural expansion, massive gene duplication, and transposable element colonization in a supergene controlling ant social organization.Molecular biology and evolution · 2026Article
- HPV16 genetic variation provides evidence of positive natural selection driven by HLA class I.Nature communications · 2026Article
- Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses.PLoS pathogens · 2026Article
- SARS-CoV-2 intra-host viral diversity associated with host innate and vaccine-induced immunity in an obese mouse model.BMC infectious diseases · 2026Article
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- Experimental evolution of the host range dynamics in two isolates of potato virus Y.Virus evolution · 2026Article
- SARS-CoV-2 within-host population expansion, diversification and adaptation in zoo tigers, lions and hyenas.Nature communications · 2025Article
- Complete genomes of Rickettsia typhi reveal a clonal population.PLoS neglected tropical diseases · 2025Article
- Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses.bioRxiv : the preprint server for biology · 2025Article
- Longitudinal analysis of influenza A virus deletion-containing viral genomes reveals key determinants of co-evolutionary dynamics and interference.bioRxiv : the preprint server for biology · 2025Article
- A Virome Scanning of Saffron (Viruses · 2025Article
- A single mutation may contribute to accelerated evolution of SARS-CoV-2 toward Omicron.Nature communications · 2025Article
- Genomic and evolutionary evidence for drought adaptation of allopolyploid Brachypodium hybridum.Journal of experimental botany · 2025Article
58 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
unlabelledNew applications of next-generation sequencing technologies use pools of DNA from multiple individuals to estimate population genetic parameters. However, no publicly available tools exist to analyse single-nucleotide polymorphism (SNP) calling results directly for evolutionary parameters important in detecting natural selection, including nucleotide diversity and gene diversity. We have developed SNPGenie to fill this gap. The user submits a FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with CDS information and a SNP report(s) in an increasing selection of formats. The program estimates nucleotide diversity, distance from the reference and gene diversity. Sites are flagged for multiple overlapping reading frames, and are categorized by polymorphism type: nonsynonymous, synonymous, or ambiguous. The results allow single nucleotide, single codon, sliding window, whole gene and whole genome/population analyses that aid in the detection of positive and purifying natural selection in the source population. AVAILABILITY AND IMPLEMENTATION: SNPGenie version 1.2 is a Perl program with no additional dependencies. It is free, open-source, and available for download at https://github.com/hugheslab/snpgenie. CONTACT: nelsoncw@email.sc.edu or austin@biol.sc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.