Minimum conflict:: a divide-and-conquer approach to phylogeny estimation

被引:10
|
作者
Fuellen, G [1 ]
Wägele, JW
Giegerich, R
机构
[1] Ruhr Univ Bochum, Lehrstuhl Spez, D-44780 Bochum, Germany
[2] Univ Bielefeld, Tech Fak, D-33594 Bielefeld, Germany
[3] Univ Munster, Integrated Funct Genom, IZKF, D-48149 Munster, Germany
关键词
D O I
10.1093/bioinformatics/17.12.1168
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Fast and reliable phylogeny estimation is rapidly gaining importance as more and more genomic sequence information is becoming available, and the study of the evolution of genes and genomes accelerates our understanding in biology and medicine alike. Branch attraction phenomena due to unequal amounts of evolutionary change in different parts of the phylogeny are one major problem for current methods, placing the species that evolved fast in one part of the phylogenetic tree, and the species that evolved slowly in the other. Results: We describe a way to avoid the artifactual attraction of species that evolved slowly, by detecting shared old character states using a calibrated comparison with an outgroup. The corresponding focus on shared novel character states yields a fast and transparent phylogeny estimation algorithm, by application of the divide-and-conquer principle, and heuristic search: shared novelties give evidence of the exclusive common heritage (monophyly) of a subset of the species. They indicate conflict in a split of all species considered, if the split tears them apart. Only the split at the root of the phylogenetic tree cannot have such conflict. Therefore, we can work top-down, from the root to the leaves, by heuristically searching for a minimum-conflict split, and tackling the resulting two subsets in the same way. The algorithm, called 'minimum conflict phylogeny estimation' (MCOPE), has been validated successfully using both natural and artificial data. In particular, we reanalyze published trees, yielding more plausible phylogenies, and we analyze small 'undisputed' trees on the basis of alignments considering structural homology.
引用
收藏
页码:1168 / 1178
页数:11
相关论文
共 50 条
  • [1] Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge
    Erin K. Molloy
    Tandy Warnow
    [J]. Algorithms for Molecular Biology, 14
  • [2] A DIVIDE-AND-CONQUER APPROACH TO LEAST-SQUARES ESTIMATION
    ABEL, JS
    [J]. IEEE TRANSACTIONS ON AEROSPACE AND ELECTRONIC SYSTEMS, 1990, 26 (02) : 423 - 426
  • [3] A divide-and-conquer approach to estimating minimum/maximum leakage current
    Liao, GW
    Feng, JS
    Lin, RB
    [J]. 2005 IEEE INTERNATIONAL SYMPOSIUM ON CIRCUITS AND SYSTEMS (ISCAS), VOLS 1-6, CONFERENCE PROCEEDINGS, 2005, : 4717 - 4720
  • [4] A Divide-and-Conquer Approach to the Minimum k -Way Cut Problem
    [J]. Algorithmica, 2002, 32 : 262 - 276
  • [5] Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation
    Yu, Xilin
    Le, Thien
    Christensen, Sarah A.
    Molloy, Erin K.
    Warnow, Tandy
    [J]. ALGORITHMS FOR MOLECULAR BIOLOGY, 2021, 16 (01)
  • [6] Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge
    Molloy, Erin K.
    Warnow, Tandy
    [J]. ALGORITHMS FOR MOLECULAR BIOLOGY, 2019, 14 (1)
  • [7] Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation
    Xilin Yu
    Thien Le
    Sarah A. Christensen
    Erin K. Molloy
    Tandy Warnow
    [J]. Algorithms for Molecular Biology, 16
  • [8] A divide-and-conquer approach to the minimum k-way cut problem
    Kamidoi, Y
    Wakabayashi, S
    Yoshida, N
    [J]. ALGORITHMICA, 2002, 32 (02) : 262 - 276
  • [9] A Divide-and-Conquer Approach for Minimum Spanning Tree-Based Clustering
    Wang, Xiaochun
    Wang, Xiali
    Wilkes, Mitchell
    [J]. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING, 2009, 21 (07) : 945 - 958
  • [10] Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood
    Du, Z
    Stamatakis, A
    Lin, F
    Roshan, U
    Nakhleh, L
    [J]. HIGH PERFORMANCE COMPUTING AND COMMUNICATIONS, PROCEEDINGS, 2005, 3726 : 776 - 785