ArticleMicrobial genomics2021
SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.
Article in Microbial genomics, 2021. 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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22 citing papers in PubMed, 24 citations in OpenAlex.
- The structural context of mutations in proteins predicts their effect on antibiotic resistance.eLife · 2026Article
- High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV.Genome research · 2026Article
- Transmission of rifampicin-resistant tuberculosis in Ho Chi Minh City, Viet Nam: a prospective genomic epidemiology study.The Lancet regional health. Western Pacific · 2026Article
- Dormancy regulon reduction was pivotal to the evolution of Mycobacterium tuberculosis.Nature communications · 2026Article
- Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss.Nature ecology & evolution · 2026Article
- The unique role ofmBio · 2026Article
- Polygenic risk and trajectories of depressive symptoms in diverse adolescents: Gene-environment interplay with family conflict and parental acceptance.Development and psychopathology · 2025Article
- Evaluating selection at intermediate scales within genes provides robust identification of genes under positive selection in M. tuberculosis clinical isolates.Tuberculosis (Edinburgh, Scotland) · 2025Article
- Unraveling Epistatic Interactions Between Sites Under Drug-Dependent Selection in the Mycobacterium tuberculosis Genome.Molecular biology and evolution · 2025Article
- High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV.bioRxiv : the preprint server for biology · 2025Article
- Evaluating selection at intermediate scales within genes provides robust identification of genes under positive selection inbioRxiv : the preprint server for biology · 2025Article
- Evolution of pathogenic Escherichia coli harboring the transmissible locus of stress tolerance: from food sources to clinical environments.Scientific reports · 2025Article
- Genomic perspective on the bacillus causing paratyphoid B fever.Nature communications · 2024Article
- Phase variation as a major mechanism of adaptation inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- The clinical features and genomic epidemiology of carbapenem-resistant Acinetobacter baumannii infections at a tertiary hospital in Vietnam.Journal of global antimicrobial resistance · 2023Article
- Analysis of Genome-Wide Mutational Dependence in Naturally Evolving Mycobacterium tuberculosis Populations.Molecular biology and evolution · 2023Article
- Mutation rates and adaptive variation among the clinically dominant clusters ofProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Persistent Salmonella enterica serovar Typhi sub-populations within host interrogated by whole genome sequencing and metagenomics.PloS one · 2023Article
- Article
- Role of Epistasis in Amikacin, Kanamycin, Bedaquiline, and Clofazimine Resistance in Mycobacterium tuberculosis Complex.Antimicrobial agents and chemotherapy · 2021Article
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Authors and funding
4 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Homoplasic SNPs are considered important signatures of strong (positive) selective pressure, and hence of adaptive evolution for clinically relevant traits such as antibiotic resistance and virulence. Here we present a new tool, SNPPar, for efficient detection and analysis of homoplasic SNPs from large whole genome sequencing datasets (>1000 isolates and/or >100 000 SNPs). SNPPar takes as input an SNP alignment, tree and annotated reference genome, and uses a combination of simple monophyly tests and ancestral state reconstruction (ASR, via TreeTime) to assign mutation events to branches and identify homoplasies. Mutations are annotated at the level of codon and gene, to facilitate analysis of convergent evolution. Testing on simulated data (120
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