Combining polynomial running time and fast convergence for the disk-covering method
Journal of Computer and System Sciences - Computational biology 2002
On the complexity of distance-based evolutionary tree reconstruction
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
Construction of Phylogenetic Trees on Parallel Clusters
PPAM '01 Proceedings of the th International Conference on Parallel Processing and Applied Mathematics-Revised Papers
The Performance of Phylogenetic Methods on Trees of Bounded Diameter
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Sequence-Length Requirements for Phylogenetic Methods
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Theoretical Computer Science
ICALP'05 Proceedings of the 32nd international conference on Automata, Languages and Programming
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We present a novel distance-based algorithm for evolutionary tree reconstruction. Our algorithm reconstructs the topology of a tree with n leaves in O(n2) time using O(n) working space. In the general Markov model of evolution the algorithm recovers the topology successfully with (1 — &Ogr;(1)) probability from sequences with polynomial length in n. Moreover, for almost all trees, our algorithm achieves the same success probability on polylogarithmic sample sizes. The theoretical results are supported by simulation experiments involving trees with 500, 1895, and 3135 leaves. The topologies of the trees are recovered with high success from 2000 bp DNA sequences.