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Updated: Nov 6, 2025
08:03
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
2.6K
Inferring Core Genome Phylogenies for Bacteria.
Alexander Keller1,2, Markus J Ankenbrand3,4,5
1Center for Computational and Theoretical Biology, Biocenter, University of Würzburg, Würzburg, Germany. a.keller@biozentrum.uni-wuerzburg.de.
Methods in Molecular Biology (Clifton, N.J.)
|May 7, 2021
Summary
Phylogenetic analysis is now feasible using multiple genes, thanks to abundant bacterial genome data. This protocol details a bioinformatic workflow for high-resolution bacterial strain and clade phylogenetic reconstructions.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Increasing availability of public bacterial genome data.
- Cost-efficiency of novel bacterial strain sequencing.
- Feasibility of phylogenetic analyses beyond single marker genes.
Purpose of the Study:
- To describe a complete bioinformatic workflow for phylogenetic analysis.
- To enable high-resolution phylogenetic reconstructions.
- To facilitate strain-level and broad clade analyses.
Main Methods:
- Utilizing raw genomic data.
- Implementing a bioinformatic workflow.
- Performing phylogenetic analyses based on 107 conserved single copy genes.
Main Results:
- A complete bioinformatic workflow from raw data to phylogenetic analysis.
- High-resolution phylogenetic reconstructions.
- Applicability across different bacterial clades and at the strain level.
Conclusions:
- The described method provides a robust approach for bacterial phylogenetic analysis.
- This workflow leverages multi-gene data for enhanced resolution.
- It is applicable for diverse phylogenetic questions in bacterial research.
Keywords:
16SBioinformaticsGenomicsHigh-performance computingMaximum likelihoodParallel computingPhylogeneticsPhylogenomicsProkaryoteSequence analysisMore Related Videos
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