Computational Phylogenetics An introduction to designing methods for phylogeny estimation
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Maximum Likelihood Methods for Phylogenetic Inference
In this article, we provide an overview of maximum likelihood methods for phylogenetic inference. A brief introduction to general maximum likelihood estimation is provided. We define a phylogenetic likelihood, summarize how to compute this likelihood, and then discuss approaches used to maximize the phylogenetic likelihood function. We discuss a property of the maximum likelihood estimation, ca...
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