Maximal accurate forests from distance matrices

Authors:
Constantinos Daskalakis;Cameron Hill;Alexandar Jaffe;Radu Mihaescu;Elehanan Mossel;Satish Rao
Affiliations:
University of California, Berkeley;University of California, Berkeley;University of California, Berkeley;University of California, Berkeley;University of California, Berkeley;University of California, Berkeley
Venue:
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Year:
2006

Citing 4
Cited 7

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
Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees

CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Distorted Metrics on Trees and Phylogenetic Forests

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

Distorted Metrics on Trees and Phylogenetic Forests

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast and reliable reconstruction of phylogenetic trees with very short edges

Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms
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)
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

Quantified Score

Hi-index	0.00

Visualization

Abstract

We present a fast converging method for distance-based phylogenetic inference, which is novel in two respects. First, it is the only method (to our knowledge) to guarantee accuracy when knowledge about the model tree, i.e bounds on the edge lengths, is not assumed. Second, our algorithm guarantees that, with high probability, no false assertions are made. The algorithm produces a maximal forest of the model tree, in time Õ(n3) in the typical case. Empirical testing has been promising, comparing favorably to Neighbor Joining, with the advantage of making few or no false assertions about the topology of the model tree; guarantees against false positives can be controlled as a parameter by the user.