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Phylogenetics Tutorial for Biochemists
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Phylogenetics is appealing to biochemists for understanding how proteins evolve, but it can be **intimidating**. 


*Where do I start? How do I create and curate a sequence alignment? What model(s) should I use when building trees, and what are these models doing anyway? How do I evaluate the quality of a tree or of ancestrally reconstructed proteins? What's with all of these obnoxious file formats?*

*If you're asking yourself any or all of these questions, this tutorial is for you. We will walk through phylogenetic analysis from start to finish.*

We use python and `jupyter notebooks`(https://github.com/jupyter/notebook) to interface with established phylogenetic packages. If you are new to using these, you can quickly get up and running [here](https://python-for-scientists.readthedocs.io/en/latest/).

:ref:`Three basic steps <basics>` for phylogenetic analysis:

- gathering and aligning sequences

- building and evaluating phylogenetic trees

- reconstructing ancestral proteins

Commonly asked questions and pitfalls:

- managing data and file formats with [phylopandas](https://github.com/Zsailer/phylopandas)

- [evaluating and curating alignments]()

- [choosing evolutionary models]()

- [including extra information in tree-building (secondary structure, etc.)]()

If you have any additional questions, [please ask]()!

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   :caption: Phylogenetics quick-start guide
   
   _pages/quick-start.rst
   
.. toctree::
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   :caption: Phylogenetics