Warnow, T., B. M. Moret, and K. S. John (2001). Absolute convergence: true trees from short sequences. In Proceedings of the Twelfth Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 186--195. ACM.  Home/Search   Document Details and Download   Summary   Related Articles   Check

....4 ) time. The statistically e#cient Fast Harmonic Greedy Triplets algorithm of Csuros and Kao (2001) also runs in O(n 2 ) time but its e#ciency is contingent upon knowing the highest mutation rate on a tree edge. A major advantage of HGT FP is that it does not rely on any such input parameter. Warnow et al. 2001) describe an algorithm that turns a statistically e#cient algorithm needing such a parameter into an algorithm that is statistically e#cient without it. The transformation, however, increases the running time of the original algorithm by O(n 4 ) 1.3 Distance based algorithms A number of ....

Warnow, T., B. M. Moret, and K. S. John (2001). Absolute convergence: true trees from short sequences. In Proceedings of the Twelfth Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 186--195. ACM.

....O(n 4 ) time. The statistically e#cient Fast Harmonic Greedy Triplets algorithm [9] also runs in O(n 2 ) time but its e#ciency is contingent upon knowing of the highest mutation rate on a tree edge. A major advantage of HGT FP is that it does not rely on any such input parameter. Warnow et al. [30] describe an algorithm that turns a statistically e#cient algorithm needing such a parameter into an algorithm that is statistically e#cient without it. The transformation, however, increases the running time of the original algorithm by O(n 4 ) 1.3 Distance based algorithms A number of ....

T. Warnow, B. M. Moret, and K. S. John. Absolute convergence: true trees from short sequences. In Twelfth Annual ACM-SIAM Symposium on Discrete Algorithms, 2001. To appear.

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T. Warnow, B. Moret, and K. St. John. Absolute convergence: true trees from short sequences. Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA 01), pages 186--195, 2001.

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T. Warnow, B. Moret, and K. St. John. Absolute convergence: true trees from short sequences. Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA 01), pages 186--195, 2001.

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T. Warnow, B. Moret, and K. St. John. Absolute convergence: true trees from short sequences. Proc. 12th ACM-SIAM Symp. on Discrete Algorithms (SODA el), pages 186-195, 2001.

....parameterization leads to the definition of fast converging methods, which are methods that recover the true tree from sequences of lengths bounded by a polynomial in n once f , the minimum edge length, and g, the maximum edge length, are bounded. Several fast converging methods were developed [3, 4, 8, 21]. We and others analyzed the sequence length requirement of standard methods, such as neighbor joining (NJ) under the assumptions that f and g are fixed. These studies [1, 6] showed that neighbor joining and many other methods can be proven to be exponentially converging , that is, they recover ....

....the sequence length has to be larger in order for neighbor joining to return the true tree with high probability. Note that the diameter of the tree and the sequence length are exponentially related. 3. 1 Fixed parameter Analyses of the Convergence Rate Analysis when both f and g are fixed: In [8, 21], the convergence rate of neighbor joining was analyzed when both f and g are fixed (recall that f is the smallest edge length, and g is the largest edge length) In this setting, by Theorem 1 and because maxl i j = O(gn) we see that neighbor joining recovers the true tree, with probability 1 e, ....

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T. Warnow, B. Moret, and K. St. John. Absolute convergence: true trees from short sequences. Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA 01), pages 186--195, 2001.

....methods, neighbor joining, maximum likelihood, maximum parsimony. 1 Introduction Performance studies of phylogenetic methods focus upon how accurately methods can reconstruct the unrooted underlying leaf labeled tree (called the topology ) under various model conditions. Recent research [8, 9, 17, 33] has developed a new class of phylogenetic methods, called fast converging methods, which provably recover the true tree topology with high probability given only polynomial length sequences. Department of Computer Sciences, University of Texas, Austin, TX 78712; 512) 471 9724; Fax: 512) ....

....of evolution. JC was chosen since the original studies [7] showing the HGT FP method outperformed NJ on large trees with high evolution were done under this model of evolution. K2P Gamma was chosen due to its popularity in many recent phylogenetic studies. Of our various afc methods, DCM NJ [33] is the best performing (the others are in [8, 9, 17] and have not performed as well as DCM NJ in our (unpublished) simulation studies) DCM NJ is not polynomial time, since it involves solving an NP hard problem, although polynomial time versions of DCM NJ in which the NP hard optimization ....

Warnow, T., Moret, B. M. E., and St. John, K., "Absolute Convergence: True Trees From Short Sequences," IEEE Symposium on Discrete Algorithms (SODA 01), pp 186--195. 12

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T. Warnow, B. Moret, and K. St. John. Absolute convergence: true trees from short sequences. Proc. 12th ACM-SIAM Symp. on Discrete Algorithms (SODA 01), pages 186--195, 2001.

No context found.

Warnow, T., B. M. Moret, and K. S. John (2001). Absolute convergence: true trees from short sequences. In Proceedings of the Twelfth Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 186--195. ACM.

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