Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.

Microbial genomics - 1 Dec 2021

Edwards David J, Duchene Sebastián, Pope Bernard, Holt Kathryn E

Abstract excerpt

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,...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Burkholderia
Share to Databases, Genetic
Share to Flavobacteriaceae

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Share to Genome, Bacterial

Share to Molecular Sequence Annotation

Share to Mycobacterium tuberculosis

Share to Software

Share to Whole Genome Sequencing

Source

Open in PubMed Open full text

Identifiers

PMID: 34874243
DOI: 10.1099/mgen.0.000694
PMCID: PMC8767352

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 3 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.PMID 34874243Read ↗

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignmentsSemantic proximity Read ↗

Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis.Semantic proximity Read ↗

Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing.Semantic proximity Read ↗

From raw reads to trees: Whole genome SNP phylogenetics across the tree of lifeSemantic proximity Read ↗

Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis.Semantic proximity Read ↗

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.Semantic proximity Read ↗

Genomic diversity affects the accuracy of bacterial SNP calling pipelinesSemantic proximity Read ↗

Evolutionary robust SNPs reveal the misclassification of Mycobacterium tuberculosis Beijing family strains into sublineages.Semantic proximity Read ↗

snpTree--a web-server to identify and construct SNP trees from whole genome sequence data.Semantic proximity Read ↗

Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru.Semantic proximity Read ↗

Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers.Semantic proximity Read ↗

Convergent evolutionary analysis identifies significant mutations in drug resistance targets of Mycobacterium tuberculosis.Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.