Gubbins

Gubbins detects recombinant regions in bacterial whole-genome sequence alignments and reconstructs maximum likelihood phylogenies from point mutations outside recombination-affected regions to infer bacterial evolutionary relationships.

Key Features:

• Iterative Algorithm: An iterative algorithm integrates spatial scanning statistics to detect loci with elevated densities of base substitutions indicative of horizontal gene transfer.
• Recombination Detection: Identifies regions affected by recombination by locating high-diversity loci characterized by clustered base substitutions.
• Phylogenetic Reconstruction: Constructs maximum likelihood phylogenies based on point mutations outside identified high-diversity (recombination-affected) regions.
• Efficiency and Scalability: Processes alignments of hundreds of bacterial genome sequences and achieves convergence in a few hours on typical datasets.
• Flexibility: Does not assume a specific mechanism of recombination and is applicable to diverse haploid genotype alignments.

Scientific Applications:

• Evolutionary studies: Resolving recent diversification and evolutionary relationships among bacterial isolates by accounting for horizontal sequence transfer.
• Outbreak analyses: Inferring clonal relationships and transmission links in outbreak investigations by removing the confounding effects of recombination.

Methodology:

Gubbins applies an iterative algorithm that uses spatial scanning statistics to identify regions with high densities of base substitutions indicative of horizontal sequence transfer, then reconstructs maximum likelihood phylogenies from point mutations outside these identified high-diversity regions and repeats the process until convergence.