# 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…

## 40,691 Citations

### CONFIDENCE LIMITS ON PHYLOGENIES: THE BOOTSTRAP REVISITED.

- BiologyCladistics : the international journal of the Willi Hennig Society
- 1989

Additional applications of the bootstrap are proposed which provide useful information about phylogeny even when many clades are found not to be supported with confidence, and the distinction between hypotheses about membership in particular clades and hypotheses about entire topologies is discussed.

### CONFIDENCE LIMITS ON PHYLOGENIES: THE BOOTSTRAP REVISITED

- Biology
- 1989

Additional applications of the bootstrap are proposed which provide useful information about phylogeny even when many clades are found not to be supported with confidence, and the distinction between hypotheses about membership in particular clades and hypotheses about entire topologies is discussed.

### A statistical test of phylogenies estimated from sequence data.

- BiologyMolecular biology and evolution
- 1989

A simple approach to testing the significance of the branching order, estimated from protein or DNA sequence data, of three taxa is proposed, and a formula for the variance of the internodal distance has been developed.

### Use of the Method of Generalized Least Squares in Reconstructing Phylogenies from Sequence Data

- Biology
- 1991

The method of generalized least squares provides a flexible method of phylogenetic reconstruction from sequence data, after reducing them to pairwise distances between species, corrected for multiple…

### Confidence Limits on Phylogenies With a Molecular Clock

- Biology
- 1985

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.

### Isolating - a new resampling method for gene order data

- Mathematics2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)
- 2011

A new method is proposed that overcomes this disadvantage of jackknifing and achieves better accuracy and confidence values for gene order data and can produce phylogenies with lower error rates and much stronger support for good branches.

### Applying the Bootstrap in Phylogeny Reconstruction

- Biology
- 2003

The usefulness of phylogenetic bootstrapping is potentially limited by a number of features, such as the size of the data matrix and the underlying assumptions of the phylogeny reconstruction program.

### The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies.

- BiologyMolecular biology and evolution
- 1992

The purpose of the present report is to explore the variance (and hence the accuracy) of the phylogenetic BP and to establish guidelines for efficient bootstrap sampling.

### Bootstrapping phylogenies inferred from rearrangement data

- BiologyAlgorithms for Molecular Biology
- 2011

This work presents a new approach to the assessment of distance-based phylogenetic inference from whole-genome data, and is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences.

### Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees

- BiologyBMC Evolutionary Biology
- 2010

The simulations conducted with two real data sets and the five weighting strategies suggest that the SBS-based bootstrapping with the data normalization usually exhibits larger bootstrap scores and a higher robustness compared to the four other competing strategies, including the traditionalbootstrapping.

## References

SHOWING 1-10 OF 12 REFERENCES

### Confidence Limits on Phylogenies With a Molecular Clock

- Biology
- 1985

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.

### Statistical inference of phylogenies

- Biology
- 1983

There are many unsolved problems, the most important of which is to persuade biologists to think of the problem of inferring phylogenies as being basically statistical, and to abandon deductive frameworks that are used as a justification for "parsimony" methods.

### Parsimony in Systematics: Biological and Statistical Issues

- Biology
- 1983

Methods of classification and methods of inferring phylogeny are of course separate issues and only the latter are discussed here.

### PHYLOGENETIC INFERENCE FROM RESTRICTION ENDONUCLEASE CLEAVAGE SITE MAPS WITH PARTICULAR REFERENCE TO THE EVOLUTION OF HUMANS AND THE APES

- BiologyEvolution; international journal of organic evolution
- 1983

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

- Mathematics
- 1979

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,…

### Computer-Intensive Methods in Statistics

- Computer Science
- 1983

The bootstrap method is examined and evaluated as an example of this new generation of statistical tools that take advantage of the high speed digital computer and free the statistician to attack more complicated problems.

### The jackknife, the bootstrap, and other resampling plans

- Mathematics
- 1987

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

- Mathematics, Computer Science
- 1981

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.