SHOT

SHOT classifies genomes by analyzing shared gene content and conservation of gene order to infer phylogenetic relationships and detect deviations attributable to horizontal gene transfer.

Key Features:

• Genomic classification: Classifies genomes using shared gene content and conservation of gene order as primary criteria.
• Genome tree construction: Generates genome trees representing species relationships derived from genomic properties.
• Phylogenetic consistency: Produces genome trees that generally align with classical gene-based phylogenies.
• Detection of horizontal gene transfer (HGT): Identifies exceptions in genome tree topologies that indicate significant HGT events.

Scientific Applications:

• Phylogenomics: Constructs genome-based trees to explore species relationships across the tree of life.
• Evolutionary biology: Detects signals of horizontal gene transfer to study non-vertical inheritance mechanisms.
• Comparative genomics: Compares genomic architectures to identify conserved genes and gene order indicative of functional or evolutionary significance.

Methodology:

Constructs genome trees and classifies genomes by quantifying shared gene content and conservation of gene order, integrating both signals to identify congruent phylogenetic relationships and exceptions indicative of horizontal gene transfer.