kamino: proteome-wide variant calling for amino acid phylogenomics (opens in new tab)

Amino acid-based phylogenetics usually relies on first clustering and aligning orthologous proteins. This approach is powerful but computationally demanding. Here, we present kamino, a reference-free and alignment-free method that builds amino acid phylogenomic alignments directly from proteomes. kamino adapts a local graph-based variant-calling algorithm to efficiently identify variable homologous positions among proteins and concatenate these polymorphic regions. Across diverse prokaryotic ...