Determining the evolutionary tree using experiments
Journal of Algorithms
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
A few logs suffice to build (almost) all trees: part II
Theoretical Computer Science
Computing the quartet distance between evolutionary trees
SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
On the complexity of distance-based evolutionary tree reconstruction
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
Noisy binary search and its applications
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Optimal implementations of UPGMA and other common clustering algorithms
Information Processing Letters
Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Large-scale neighbor-joining with NINJA
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Fast error-tolerant quartet phylogeny algorithms
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
ICALP'05 Proceedings of the 32nd international conference on Automata, Languages and Programming
Fast phylogenetic tree reconstruction using locality-sensitive hashing
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Fast error-tolerant quartet phylogeny algorithms
Theoretical Computer Science
| Hi-index | 0.00 |
Recently, we have identified a quartet phylogeny algorithm with O(n log n) expected runtime, which is asymptotically optimal. Regardless of the true topology, our algorithm has high probability of returning the correct phylogeny when quartet errors are independent and occur with known probability, and when the algorithm uses a guide tree on O(log log n) taxa that is correct with high probability. In practice, none of these assumptions is correct: quartet errors are positively correlated and occur with unknown probability, and the guide tree is often error prone. Here, we bring our work out of the purely theoretical setting. We present a variety of extensions which, while only slowing the algorithm down by a constant factor, make its performance nearly comparable to that of neighbour-joining, which requires O(n3) runtime. Our results suggest a new direction for quartet-based phylogenetic reconstruction that may yield striking speed improvements at minimal accuracy cost.