Why Neighbor-Joining Works

@article{Mihaescu2007WhyNW,
  title={Why Neighbor-Joining Works},
  author={Radu Mihaescu and D. Levy and L. Pachter},
  journal={Algorithmica},
  year={2007},
  volume={54},
  pages={1-24}
}
Abstract We show that the neighbor-joining algorithm is a robust quartet method for constructing trees from distances. This leads to a new performance guarantee that contains Atteson’s optimal radius bound as a special case and explains many cases where neighbor-joining is successful even when Atteson’s criterion is not satisfied. We also provide a proof for Atteson’s conjecture on the optimal edge radius of the neighbor-joining algorithm. The strong performance guarantees we provide also hold… Expand

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References

SHOWING 1-10 OF 44 REFERENCES
Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates.
TLDR
A generalization of the neighbor- joining transformation is presented, which uses estimates of phylogenetic diversity rather than pairwise distances in the tree, which leads to an improved neighbor-joining algorithm whose total running time is still polynomial in the number of taxa. Expand
Fast Neighbor Joining
TLDR
Initial experiments show that FNJ in practice has almost the same accuracy as NJ, indicating that the property of optimal reconstruction radius has great importance to their good performance. Expand
The Performance of Neighbor-Joining Methods of Phylogenetic Reconstruction
TLDR
An upper bound on the amount of data necessary to reconstruct the topology with high confidence is demonstrated by finding conditions under which these methods will determine the correct tree topology and showing that these perform as well as possible in a certain sense. Expand
On the Uniqueness of the Selection Criterion in Neighbor-Joining
  • D. Bryant
  • Mathematics, Computer Science
  • J. Classif.
  • 2005
TLDR
It is shown that any selection criterion that is linear, permutation equivariant, statistically consistent and based solely on distance data will give the same trees as those created by NJ. Expand
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
TLDR
The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data. Expand
Neighbor-joining revealed.
TLDR
A rigorous answer to this question has recently been provided by further mathematical investigation, and the purpose of this note is to highlight these results and their significance for interpreting NJ. Expand
NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods.
  • S. Ota, W. Li
  • Biology, Medicine
  • Molecular biology and evolution
  • 2000
TLDR
A "divide-and-conquer" heuristic algorithm in which an initial neighbor-joining (NJ) tree is divided into subtrees at internal branches having bootstrap values higher than a threshold, which is suitable for reconstructing relatively large molecular phylogenetic trees. Expand
Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining
TLDR
The experimental results and theoretical results suggest that quartet-cleaning methods are unlikely to yield accurate trees with less than exponentially long sequences, and suggest that a proposed reconstruction method should first be compared to the neighbor-joining method and further studied only if it offers a demonstrable practical advantage. Expand
On the edge linfinitf radius of Saitou and Nei's method for phylogenetic reconstruction
TLDR
The performance of Saitou and Nei's neighbor-joining method for phylogenetic reconstruction is studied to show that the edge l∞ radius of the method is 1/4, which improves an result by Atteson and Xu. Expand
A lower bound on the edge linfinitely radius of Saitou and Nei's method for phylogenetic reconstruction
TLDR
The performance of Saitou and Nei's neighbor-joining method for phylogenetic reconstruction is studied to show that the edge linfin; radius of the method is at least 1/6. Expand
...
1
2
3
4
5
...