Section 3 Cogent3

Cogent3 and its apps

NOTE There's a screen recording of this part of the workshop.

Cogen3 is a software library designed for molecular evolutionary analysis. It is ~20 years old and includes a comprehensive collection of tools for manipulating genomic data and performing molecular evolutionary analyses focused on modelling sequence divergence.

In this workshop, we are focusing on the library's data wrangling capabilities. We will be using it interactively within a Jupyter Notebook, so it's time to create one of those within VS Code.

Open the VS Code command palette – ^+shift+p (Windows, Linux) or command+shift+p (macOS), or you can select `"View > Command Palette..." in the GUI. Start typing "jupyter" and you should see "Create: New Jupyter Notebook", navigate to that choice via arrow keys or mouse and select it (enter key, or mouse click). Click on the "Select Kernel" text in the top right of the window, then "Python Environments..." and choose c312.

As a demo, let's do a simple plotly figure, just to make sure everything is working well.

import plotly.express as px

fig = px.scatter(x=[1, 2, 3], y=[4, 5, 6], width=600, height=600)
fig.show()

If that's going well, let's get started with inspecting the ortholog data.