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Accuracy guarantees for phylogeny reconstruction algorithms based on balanced minimum evolution.

Bordewich, M. and Mihaescu, R. (2013) 'Accuracy guarantees for phylogeny reconstruction algorithms based on balanced minimum evolution.', IEEE/ACM transactions on computational biology and bioinformatics., 10 (3). pp. 576-583.

Abstract

Distance-based phylogenetic methods attempt to reconstruct an accurate phylogenetic tree from an estimated matrix of pairwise distances between taxa. This paper examines two distance-based algorithms (GREEDYBME and FASTME) that are based on the principle of minimizing the balanced minimum evolution score of the output tree in relation to the given estimated distance matrix. This is also the principle that underlies the neighbor-joining (NJ) algorithm. We show that GREEDYBME and FASTME both reconstruct the entire correct tree if the input data are quartet consistent, and also that if the maximum error of any distance estimate is ϵ, then both algorithms output trees containing all sufficiently long edges of the true tree: those having length at least 3ϵ. That is to say, the algorithms have edge safety radius 1/3. In contrast, quartet consistency of the data is not sufficient to guarantee the NJ algorithm reconstructs the correct tree, and moreover, the NJ algorithm has edge safety radius of 1/4: Only edges of the true tree of length at least 4ϵ can be guaranteed to appear in the output. These results give further theoretical support to the experimental evidence suggesting FastME is a more suitable distance-based phylogeny reconstruction method than the NJ algorithm.

Item Type:Article
Full text:(AM) Accepted Manuscript
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Status:Peer-reviewed
Publisher Web site:http://dx.doi.org/10.1109/TCBB.2013.39
Publisher statement:© 2013 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Date accepted:No date available
Date deposited:20 April 2016
Date of first online publication:May 2013
Date first made open access:No date available

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