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.


Article metrics loading...

Loading full text...

Full text loading...


Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error