B. DasGupta, X. He, T. Jiang, M. Li, J. Tromp, and L. Zhang, On computing the nearest neighbor interchange distance, In: Discrete Mathematical Problems with Medical Applications, New Brunswick, NJ, 1999, DIMACS Ser. Discrete Math. Theoret. Comput. Sci., Vol. 55, Amer. Math. Soc., Providence, RI, 2000, pp. 125--143. Home/Search Document Details and Download
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On the Linear-Cost Subtree-Transfer Distance between.. - Bhaskar Dasgupta Self-citation (Dasgupta He Jiang Li Tromp) (Correct)
.... Comparison of weighted phylogenies has recently been studied in [16] The distance measure adopted is based on the difference in the partitions of the leaves induced by the edges in both trees, and has the drawback of being somewhat insensitive to the tree topologies [8] Just like the nni model [4], the linear cost subtree transfer model can be naturally extended to weighted phylogenies: a moving subtree is charged for the weighted distance it travels. Intuitively this measure is more sensitive to the tree topologies than the one in [16] In this paper, we study the computational complexity ....
....and weighted phylogenies. The rest of the paper is organized as follows. In section 1.1, we show that the linear cost subtree transfer distance is in fact identical to the nni distance on unweighted phylogenies. As a result, the complexity and approximation results for the nni distance reported in [3, 4] directly apply to the linear cost subtree2 s 1 s 2 s 3 s 4 s 1 s 2 s 3 s 4 s 2 s 2 s 1 s 2 s 3 s 4 One subtree transfer tree for left part of tree for right part of (b) a) 2 1 1 1 rp 1 2 4 4 2 3 Figure 3: 13] Recombination event at point rp in (a) corresponds to transferring subtree s 2 in ....
[Article contains additional citation context not shown here]
B. DasGupta, X. He, T. Jiang, M. Li, J. Tromp and L. Zhang, On Computing the Nearest Neighbor Interchange Distance, Preprint, 1997.
On the Linear-Cost Subtree-Transfer Distance between.. - DasGupta, He, Jiang, .. (1997) Self-citation (Dasgupta He Jiang Li Tromp) (Correct)
.... Comparison of weighted phylogenies has recently been studied in [14] The distance measure adopted is based on the difference in the partitions of the leaves induced by the edges in both trees, and has the drawback of being somewhat insensitive to the tree topologies [6] Just like the nni model [3], the linear cost subtree transfer model can be naturally extended to weighted phylogenies: a moving subtree is charged for the weighted distance it travels. Intuitively this measure is more sensitive to the tree topologies than the one in [14] In this paper, we study the computational complexity ....
....and weighted phylogenies. The rest of the paper is organized as follows. In section 2, we show that the linear cost subtreetransfer distance is in fact identical to the nni distance on unweighted phylogenies. As a result, the complexity and approximation results for the nni distance reported in [2, 3] directly apply to the linear cost subtree transfer distance on unweighted phylogenies too. Section 3 presents an algorithm to compute an optimal linear cost subtree transfer sequence on unweighted phylogenies in time O(n 2 log n n Delta 2 O(d) where d stands for the linear cost ....
[Article contains additional citation context not shown here]
B. DasGupta, X. He, T. Jiang, M. Li, J. Tromp and L. Zhang, On Computing the Nearest Neighbor Interchange Distance, Preprint, 1997.
Computing Distances between Evolutionary Trees - DasGupta, He, Jiang, Li.. (1998) Self-citation (Dasgupta He Jiang Li Tromp Zhang) (Correct)
....algorithm with approximation ratio of 2 was given. But given two individual pair of trees, computing the nni distance between them (either for labeled or unlabeled trees) has been a long standing open question until recently when this problem was settled (for both labeled and unlabeled trees) in [7, 9]. Theorem 1 Computing the nni distance (between two labeled or unlabeled trees) is NP complete. We provide a rough sketch of the proof of Theorem 1 for labeled trees (which is the more difficult case) The proof is by a reduction from Exact Cover by 3 Sets (X3C) which is known to be NP complete ....
....the reduction and thus the proof of Theorem 1. Lemma 3 The set S has no exact cover iff D nni (T 1 ; T 2 ) N m 2 =2, where N = q(log m logn) qm 2 28nm 4 Gamma 28n O(q) 3nM (k 2 6k)m 3 log m O(1) We provide an informal sketch of the proof of Lemma 3; the reader is referred to [7, 9] for more formal proofs. Assume that we have an exact cover for S. First, we show that the one way circuit in Figure 6 behaves as was claimed. This can be seen as follows. The counterpart of the one way circuit in T 2 is as shown in Figure 6(ii) Consider any optimal transformation of circuit (i) ....
[Article contains additional citation context not shown here]
B. DasGupta, X. He, T. Jiang, M. Li, J. Tromp, and L. Zhang, On computing the nearest neighbor interchange distance, Preprint, 1997.
The Splits in the Neighborhood of a Tree - Bryant (2004) (Correct)
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B. DasGupta, X. He, T. Jiang, M. Li, J. Tromp, and L. Zhang, On computing the nearest neighbor interchange distance, In: Discrete Mathematical Problems with Medical Applications, New Brunswick, NJ, 1999, DIMACS Ser. Discrete Math. Theoret. Comput. Sci., Vol. 55, Amer. Math. Soc., Providence, RI, 2000, pp. 125--143.
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