Bioinformatics with Python Cookbook - Second Edition

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Most of the work here can probably be performed with Biopython, but DendroPy has additional functionalities that will be explored in later recipes. Furthermore, as you will see, it's more robust with certain tasks (such as file parsing). Most importantly, there is another Python library to perform phylogenetics that you should consider. It's called ETE, and is available at http://etetoolkit.org/.