CAFE

CAFE computes alignment-free k-mer-based dissimilarity measures for genome and metagenome comparisons to quantify sequence similarity for comparative and evolutionary analyses.

Key Features:

• Diverse Dissimilarity Measures: Computes a suite of 28 alignment-free distance/dissimilarity metrics including conventional k-mer count measures, background-adjusted k-mer count measures, and presence/absence-based k-mer metrics.
• Efficiency and Scalability: Optimized for rapid calculation of k-mer-based dissimilarities, providing a faster alternative to methods such as CVTree, d2*, and d2S for large-scale genomic analyses.
• Versatile Input Compatibility: Accepts assembled genome sequences and unassembled next-generation sequencing (NGS) shotgun reads as input.
• Standardized Output Format: Exports pairwise dissimilarity results in PHYLIP format for downstream phylogenetic or comparative analyses.
• Visualization Capabilities: Provides analyses formatted for visualization as dendrograms, heatmaps, principal coordinate analysis (PCoA), and network displays to aid interpretation of pairwise dissimilarities.

Scientific Applications:

• Comparative Genomics: Quantifies genomic content similarity across species or strains using alignment-free k-mer dissimilarities.
• Metagenome Analysis: Compares microbial community composition from environmental or shotgun sequencing samples without requiring assembly.
• Evolutionary and Horizontal Gene Transfer Studies: Supports investigation of evolutionary dynamics and potential horizontal gene transfer events through k-mer-based distance measures.

Methodology:

Computations are based on k-mer analysis computing 28 alignment-free distance/dissimilarity measures, specifically using conventional k-mer counts, background-adjusted k-mer counts, and presence/absence k-mer metrics.