Abstract
One of the strengths of the maximum likelihood method of phylogenetic estimation is the ease with which hypotheses can be formulated and tested. Maximum likelihood analysis of DNA and amino acid sequence data has been made practical with recent advances in models of DNA substitution, computer programs, and computational speed. Here, we describe the maximum likelihood method and the recent improvements in models of substitution. We also describe how likelihood ratio tests of a variety of biological hypotheses can be formulated and tested using computer simulation to generate the null distribution of the likelihood ratio test statistic.
Keywords
Maximum likelihoodLikelihood-ratio testMaximum likelihood sequence estimationSubstitution (logic)StatisticsRestricted maximum likelihoodNull hypothesisStatisticScore testPhylogenetic treeComputer scienceNull (SQL)Test statisticStatistical hypothesis testingLikelihood functionLikelihood principleMathematicsEconometricsBiologyData miningQuasi-maximum likelihoodGenetics
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Publication Info
- Year
- 1997
- Type
- article
- Volume
- 28
- Issue
- 1
- Pages
- 437-466
- Citations
- 1064
- Access
- Closed
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Cite This
John P. Huelsenbeck,
Keith A. Crandall
(1997).
Phylogeny Estimation and Hypothesis Testing Using Maximum Likelihood.
Annual Review of Ecology and Systematics
, 28
(1)
, 437-466.
https://doi.org/10.1146/annurev.ecolsys.28.1.437
Identifiers
- DOI
- 10.1146/annurev.ecolsys.28.1.437