Bootstrapping phylogenetic trees: Theory and methods

被引:99
|
作者
Holmes, S [1 ]
机构
[1] Stanford Univ, Dept Stat, Stanford, CA 94305 USA
[2] INRA, Dept Biometry, Montpellier, France
关键词
bootstrap; phylogenetic trees; confidence regions; nonpositive curvature;
D O I
10.1214/ss/1063994979
中图分类号
O21 [概率论与数理统计]; C8 [统计学];
学科分类号
020208 ; 070103 ; 0714 ;
摘要
This is a survey of the use of the bootstrap in the area of systematic and evolutionary biology. I present the current usage by biologists of the bootstrap as a tool both for making inferences and for evaluating robustness, and propose a framework for thinking about these problems in terms of mathematical statistics.
引用
收藏
页码:241 / 255
页数:15
相关论文
共 50 条
  • [1] Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees
    Makarenkov, Vladimir
    Boc, Alix
    Xie, Jingxin
    Peres-Neto, Pedro
    Lapointe, Francois-Joseph
    Legendre, Pierre
    [J]. BMC EVOLUTIONARY BIOLOGY, 2010, 10
  • [2] Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees
    Vladimir Makarenkov
    Alix Boc
    Jingxin Xie
    Pedro Peres-Neto
    François-Joseph Lapointe
    Pierre Legendre
    [J]. BMC Evolutionary Biology, 10
  • [3] Coalescent methods for estimating phylogenetic trees
    Liu, Liang
    Yu, Lili
    Kubatko, Laura
    Pearl, Dennis K.
    Edwards, Scott V.
    [J]. MOLECULAR PHYLOGENETICS AND EVOLUTION, 2009, 53 (01) : 320 - 328
  • [4] BOOTSTRAPPING A METHOD OF PHYLOGENETIC INFERENCE
    NAVIDI, WC
    [J]. JOURNAL OF STATISTICAL PLANNING AND INFERENCE, 1995, 43 (1-2) : 169 - 184
  • [5] Do phylogenetic methods produce trees with biased shapes?
    Huelsenbeck, JP
    Kirkpatrick, M
    [J]. EVOLUTION, 1996, 50 (04) : 1418 - 1424
  • [6] Tie trees generated by distance methods of phylogenetic reconstruction
    Takezaki, N
    [J]. MOLECULAR BIOLOGY AND EVOLUTION, 1998, 15 (06) : 727 - 737
  • [7] Methods for automatic reference trees and multilevel phylogenetic placement
    Czech, Lucas
    Barbera, Pierre
    Stamatakis, Alexandros
    [J]. BIOINFORMATICS, 2019, 35 (07) : 1151 - 1158
  • [8] Constructing, bootstrapping, and comparing morphometric and phylogenetic trees: A case study of new world monkeys (Platyrrhini, Primates)
    Couette, S
    Escarguel, G
    Montuire, S
    [J]. JOURNAL OF MAMMALOGY, 2005, 86 (04) : 773 - 781
  • [9] Comparison of three methods for estimating internal support on phylogenetic trees
    Mort, ME
    Soltis, PS
    Soltis, DE
    Mabry, ML
    [J]. SYSTEMATIC BIOLOGY, 2000, 49 (01) : 160 - 171
  • [10] Some statistical methods for phylogenetic trees with application to HIV disease
    Critchlow, DE
    Li, SY
    Nourijelyani, K
    Pearl, DK
    [J]. MATHEMATICAL AND COMPUTER MODELLING, 2000, 32 (1-2) : 69 - 81