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

@article{Daskalakis2011AlignmentFreePR,
  title={Alignment-Free Phylogenetic Reconstruction: Sample Complexity via a Branching Process Analysis},
  author={Constantinos Daskalakis and S{\'e}bastien Roch},
  journal={ArXiv},
  year={2011},
  volume={abs/1109.5002}
}
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. 

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