Daskalakis, Constantinos et Roch, Sebastien, Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis, Annals of applied probability , 23(2), 2013, pp. 639-721
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.