Efficient algorithms for inverting evolution
STOC '96 Proceedings of the twenty-eighth annual ACM symposium on Theory of computing
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
Determining the evolutionary tree
SODA '90 Proceedings of the first 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
Provably Fast and Accurate Recovery of Evolutionary Trees through Harmonic Greedy Triplets
SIAM Journal on Computing
Balanced randomized tree splitting with applications to evolutionary tree constructions
STACS'99 Proceedings of the 16th annual conference on Theoretical aspects of computer science
On the longest path algorithm for reconstructing trees from distance matrices
Information Processing Letters
Fast and reliable reconstruction of phylogenetic trees with very short edges
Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms
Learning and Verifying Graphs Using Queries with a Focus on Edge Counting
ALT '07 Proceedings of the 18th international conference on Algorithmic Learning Theory
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
Network delay inference from additive metrics
Random Structures & Algorithms
Fast error-tolerant quartet phylogeny algorithms
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Towards a practical O(n log n) phylogeny algorithm
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Alignment-Free phylogenetic reconstruction
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Fast and reliable reconstruction of phylogenetic trees with indistinguishable edges
Random Structures & Algorithms
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
Graph reconstruction via distance oracles
ICALP'13 Proceedings of the 40th international conference on Automata, Languages, and Programming - Volume Part I
Tree topology inference from leaf-to-leaf path lengths using Prüfer sequence
International Journal of Communication Networks and Distributed Systems
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We give the first tight lower bounds on the complexity of reconstructing k-ary evolutionary trees from additive distance data. We also consider the problem under DNA-based distance estimation assumptions, where the accuracy of distance data depends on the length of the sequence and the distance. We give the first o(n2) algorithm to reconstruct trees in this context, and prove a trade-off between the length of the DNA sequences and the number of distance queries needed to reconstruct the tree. We introduce new computational models for understanding this problem, which simplify the development of algorithms. We prove lower bounds in these models which apply to the type of techniques currently in use.