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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 ofdoi:10.1146/annurev.ecolsys.28.1.437 fatcat:q3gt6km2dra7hculf3eacowpzu