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
The Performance of Phylogenetic Methods on Trees of Bounded Diameter
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Estimating Large Distances in Phylogenetic Reconstruction
WAE '99 Proceedings of the 3rd International Workshop on Algorithm Engineering
Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood
HPCC'05 Proceedings of the First international conference on High Performance Computing and Communications
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We study the sequence lengths required by neighbor-joining, greedy parsimony, and a phylogenetic reconstruction method (DCMNJ+MP) based on disk-covering and the maximum parsimony criterion. We use extensive simulations based on random birth-death trees, with controlled deviations from ultrametricity, to collect data on the scaling of sequence-length requirements for each of the three methods as a function of the number of taxa, the rate of evolution on the tree, and the deviation from ultrametricity. Our experiments show that DCMNJ+MP has consistently lower sequence-length requirements than the other two methods when trees of high topological accuracy are desired, although all methods require much longer sequences as the deviation from ultrametricity or the height of the tree grows. Our study has significant implications for large-scale phylogenetic reconstruction (where sequencelength requirements are a crucial factor), but also for future performance analyses in phylogenetics (since deviations from ultrametricity are proving pivotal).