Analyzing algorithms by simulation: variance reduction techniques and simulation speedups
ACM Computing Surveys (CSUR)
A few logs suffice to build (almost) all trees: part II
Theoretical Computer Science
A few logs suffice to build (almost) all trees (l): part I
Random Structures & Algorithms
Recovering evolutionary trees through harmonic greedy triplets
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
Absolute convergence: true trees from short sequences
SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
Fast recovery of evolutionary trees with thousands of nodes
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Inferring Evolutionary Trees with Strong Combinatorial Evidence
COCOON '97 Proceedings of the Third Annual International Conference on Computing and Combinatorics
Sequence-Length Requirements for Phylogenetic Methods
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
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We study the convergence rates of neighbor-joining and several new phylogenetic reconstruction methods on families of trees of bounded diameter. Our study presents theoretically obtained convergence rates, as well as an empirical study based upon simulation of evolution on random birth-death trees. We find that the new phylogenetic methods offer an advantage over the neighbor-joining method, except at low rates of evolution where they have comparable performance. The improvement in performance of the new methods over neighbor-joining increases with the number of taxa and the rate of evolution.