Improved Phylogeny Comparisons: Non-Shared Edges Nearest Neighbor Interchanges, and Subtree Transfers
<|reference_start|>Improved Phylogeny Comparisons: Non-Shared Edges Nearest Neighbor Interchanges, and Subtree Transfers: The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest neighbor interchange (NNI) distance. In this paper, we give the first subquadratic-time algorithm for finding the non-shared edges, which are then used to speed up the existing approximating algorithm for the NNI distance from $O(n^2)$ time to $O(n \log n)$ time. Another popular distance metric for phylogenies is the subtree transfer (STT) distance. Previous work on computing the STT distance considered degree-3 trees only. We give an approximation algorithm for the STT distance for degree-$d$ trees with arbitrary $d$ and with generalized STT operations.<|reference_end|>
@article{hon2002improved,
    title={Improved Phylogeny Comparisons: Non-Shared Edges Nearest Neighbor
  Interchanges, and Subtree Transfers},
    author={Wing-Kai Hon, Ming-Yang Kao, Tak-Wah Lam, Wing-Kin Sung, Siu-Ming Yiu},
    journal={arXiv preprint arXiv:cs/0211009},
    year={2002},
    archivePrefix={arXiv},
    eprint={cs/0211009},
    primaryClass={cs.DS}
}