Jupyter Notebook Intro

The use cases described in this manual are also provided as functional IPython Notebooks which can be downloaded from ReproPhylo github. They are downloaded by default when you use a Docker container with the startRP script. An IPython Notebook consists of formatted text (markdown) cells, which contain comments and explanations, but do not affect the program. Actual script is written in code cells, which have a shaded background. The code in the code cells can be executed (run) by placing the cursor anywhere inside a code cell and clicking shift+enter.