Alignment-Free Phylogenetic Reconstruction: Sample Complexity via a Branching Process Analysis

We present an efficient phylogenetic reconstruction algorithm, allowing insertions and deletions, which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is distance-based, that is, it relies on pairwise sequence comparisons. More importantly, our approach largely bypasses the difficult problem of multiple sequence alignment.