CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

@article{Felsenstein1985CONFIDENCELO,
  title={CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP},
  author={Joseph Felsenstein},
  journal={Evolution},
  year={1985},
  volume={39}
}
The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper… 
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References

SHOWING 1-10 OF 16 REFERENCES
Confidence Limits on Phylogenies With a Molecular Clock
TLDR
This analysis extends the pioneering work of Cavender (1978, 1981) by taking advantage of the constraints imposed by the assumption of a molecular clock to compute how many steps a phylogeny must have to be significantly worse than the most parsimonious phylogeny.
A METHOD FOR DEDUCING BRANCHING SEQUENCES IN PHYLOGENY
With the advent of relatively objective classifications, such as the phenetic classifications produced by the operational techniques of numerical taxonomy (Sokal and Sneath, 1963), it was inevitable
Parsimony in Systematics: Biological and Statistical Issues
TLDR
Methods of classification and methods of inferring phylogeny are of course separate issues and only the latter are discussed here.
Tests of phylogenetic hypotheses under generalized models
TLDR
Prospective topologies of phylogenetic trees can be tested as hypotheses using statistics based on parsimony if the unknown branch lengths of the trees are different for different characters, and when the transition probabilities between the states of characters are unequal in a known or unknown degree.
PHYLOGENETIC INFERENCE FROM RESTRICTION ENDONUCLEASE CLEAVAGE SITE MAPS WITH PARTICULAR REFERENCE TO THE EVOLUTION OF HUMANS AND THE APES
  • A. Templeton
  • Biology, Medicine
    Evolution; international journal of organic evolution
  • 1983
TLDR
An algorithm of phylogenetic inference that deals more directly with the problem of convergent evolution and statistical inhomogeneity between different restriction enzymes is proposed and non-parametric statistical procedures are presented for testing hypotheses about relative rates of evolution among the various lineages.
Bootstrap Methods: Another Look at the Jackknife
We discuss the following problem given a random sample X = (X 1, X 2,…, X n) from an unknown probability distribution F, estimate the sampling distribution of some prespecified random variable R(X,
Taxonomy with confidence
Abstract There are essentially three ways in which four species may be related in a phylogenetic tree graph. It is usual to compute for each of these three possibilities the smallest number of
Computer-Intensive Methods in Statistics
In the past few years there has been a surge in the development of new statistical theories and methods that take advantage of the high speed digital computer. The payoff for such intensive
The jackknife, the bootstrap, and other resampling plans
The Jackknife Estimate of Bias The Jackknife Estimate of Variance Bias of the Jackknife Variance Estimate The Bootstrap The Infinitesimal Jackknife The Delta Method and the Influence Function
Consensusn-trees
TLDR
A method is presented, called majority rule, which can be used to define a consensus of these classifications, and some mathematical properties of this consensus tree are discussed.
...
1
2
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