kamino: fast proteome-wide variant calling for amino acid phylogenomics.

kamino provides a fast, alignment-free method that accurately recovers phylogenetic relationships across diverse prokaryotic and eukaryotic datasets.

• Why it matters: Current amino acid-based phylogenetics relies on computationally demanding clustering and alignment, limiting scalability and speed, especially for large or complex datasets.
• What they did: kamino uses shared flanking sequences and local k-mer occupancy changes to identify homologous regions and extract pseudo-aligned sequences from proteomes, enabling rapid phylogenomic analysis.
• The result: kamino achieves comparable runtimes to genome-based alignment-free methods, is several orders of magnitude faster than classical pipelines, and performs well across various divergence levels, facilitating broad evolutionary studies.