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.
"Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis." Ann. Appl. Probab. 23 (2) 693 - 721, April 2013. https://doi.org/10.1214/12-AAP852