A fast algorithm for constructing trees from distance matrices
Information Processing Letters
Faster reliable phylogenetic analysis
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
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
Introduction to Algorithms
Evolutionary Trees Can be Learned in Polynomial Time in the Two-State General Markov Model
SIAM Journal on Computing
On the complexity of distance-based evolutionary tree reconstruction
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
Optimal phylogenetic reconstruction
Proceedings of the thirty-eighth annual ACM symposium on Theory of computing
Distorted Metrics on Trees and Phylogenetic Forests
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Maximal accurate forests from distance matrices
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
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
Reconstructing approximate phylogenetic trees from quartet samples
SODA '10 Proceedings of the twenty-first annual ACM-SIAM symposium on Discrete Algorithms
Quartets MaxCut: A Divide and Conquer Quartets Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast error-tolerant quartet phylogeny algorithms
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
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
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Phylogenetic reconstruction is the problem of reconstructing an evolutionary tree from sequences corresponding to leaves of that tree. A central goal in phylogenetic reconstruction is to be able to reconstruct the tree as accurately as possible from as short as possible input sequences. The sequence length required for correct topological reconstruction depends on certain properties of the tree, such as its depth and minimal edge-weight. Fast converging reconstruction algorithms are considered state-of the-art in this sense, as they require asymptotically minimal sequence length in order to guarantee (with high probability) correct topological reconstruction of the entire tree. However, when the original phylogenetic tree contains very short edges, this minimal sequence-length is still too long for practical purposes. Short edges are not only very hard to reconstruct; their presence may also prevent the correct reconstruction of long edges. In this paper we present a fast converging reconstruction algorithm which returns a partially resolved topology containing all edges of the original tree whose weight exceeds some (non-trivial) lower bound, which is determined by the input sequence length, as well as some properties of the tree, such as its depth. It does not depend, however, on the minimal edge-weight. This lower bound provides a partial reconstruction guarantee which is strictly stronger than the guarantees given by other fast converging algorithms. Our algorithm also has optimal complexity (linear space and quadratic-time) which, together with its partial reconstruction guarantee, makes it appealing for practical use.