Tutorial 0a: Configuring your computer | This tutorial will walk you through how to install a Python 3.6 scientific computing environment. [.ipynb file]

Tutorial 0b: Using the Jupyter notebook | This tutorial will teach you how to write code and text in Jupyter notebooks. [.ipynb file]

Tutorial 0c: A Primer on Python Syntax | This tutorial will walk you through the basics of programming in Python. [.ipynb file]

Tutorials

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Tutorial 01: Consider the Leviathan's teeth | In this tutorial we will explore the sequencing data for the ENAM gene in placental mammals. [.ipynb file]

Tutorial 02: Molecular evidence of long journeys | In this tutorial we will ask the question about the origin of a species given what the molecular evidence tells us. [.ipynb file]

Tutorial 03: Stochastic simulations of genetic drift | In this tutorial we learn how to do basic stochastic simuations to analyze the evolution of allele frequencies over time subjected to genetic drift. NOTE: The images are not rendring in the HTML version, so make sure you check the ipynb too. [.ipynb file]

Tutorial 04: Luria Delbruck Experiment. | This tutorial explores computationally the consequences of the competing hypothesis in the famous Luria-Delbrück experiment [.ipynb file]

Data Sets

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[ Sequence alignment of ENAM gene ] | This dataset is used for Tutorial 01. It contains a multiple sequence alignment of the ENAM gene of several placental mammals.

[ Sequence alignment of Mabuya sp. ] | This dataset is used for Tutorial 02. It contains a multiple sequence alignment of DNA coming from different skink species.

Useful functions

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[bar3.py] | Function to plot 3D bar plots.

In-class Exercises

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