ArticleScientific reports2016
Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- CAKR: commutative algebra k-mer representations for genomics.Nature communications · 2026Article
- Estimating Genome-Wide Phylogenies Using Probabilistic Topic Modeling.Systematic biology · 2025Article
- Transmission pathways of Campylobacter jejuni between humans and livestock in rural Ethiopia are highly complex and interdependent.Gut pathogens · 2025Article
- An alignment-free method for phylogeny estimation using maximum likelihood.BMC bioinformatics · 2025Article
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- PhageGE: an interactive web platform for exploratory analysis and visualization of bacteriophage genomes.GigaScience · 2024Article
- Genomic Diversity, Antimicrobial Resistance, Plasmidome, and Virulence Profiles ofAntibiotics (Basel, Switzerland) · 2023Article
- Synonymous nucleotide changes drive papillomavirus evolution.Tumour virus research · 2022Review
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- Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions.Frontiers in plant science · 2022Article
- CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase.Bioinformatics (Oxford, England) · 2021Article
- Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history.BMC genomics · 2021Article
- Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Comparative Genomics Supports That Brazilian BioethanolFrontiers in microbiology · 2021Article
- Long Tandem Arrays ofInternational journal of molecular sciences · 2020Article
- 'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.NAR genomics and bioinformatics · 2020Article
- UniqueInternational journal of molecular sciences · 2020Article
- Article
- KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis.Frontiers in bioengineering and biotechnology · 2020Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution.
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