KoT

KoT applies the K/θ ratio to delimit species by comparing average between-clade genetic distance (K) to within-clade genetic diversity (θ).

Key Features:

• Automated K/θ calculation: Automates computation of the K/θ ratio across clades to apply the K/θ species-delimitation method at scale.
• Input and tree construction: Accepts sequence input in FASTA format and constructs a neighbor-joining tree to approximate evolutionary distances.
• Customizable threshold: Allows specification of a K/θ threshold to determine species boundaries.
• Per-clade diversity metrics: Computes average between-clade distance (K) and within-clade genetic diversity (θ) for clades in the phylogeny.

Scientific Applications:

• Species delimitation: Identifies putative species boundaries using the K/θ criterion applied to phylogenetic clades.
• Speciation studies: Supports analyses of divergence patterns relevant to speciation by quantifying between- and within-clade genetic distances.
• Genetic diversity assessment: Enables evaluation of within-clade genetic diversity (θ) across sampled taxa.
• Conservation prioritization: Provides quantitative delimitation results that can inform conservation and biodiversity assessments.

Methodology:

Construct a neighbor-joining tree from FASTA sequence input, calculate average between-clade distance K and within-clade diversity θ for clades, compute the K/θ ratio per clade, and apply a user-specified K/θ threshold to delimit species.