COCOA-Tree: COllaborative COevolution Analysis Toolbox

COCOA-Tree is a Python library to perform coevolution analysis of protein sequence data. It includes different coevolution metrics and corrections, and allows for an easy comparison of the methods.

The specificity of COCOA-Tree is the inclusion of a visualization tool that allows the user to confront coevolution analyses with a phylogenetic tree and metadata to facilitate the understanding of protein sectors.

COCOA-Tree also provides integration with the molecular visualization software PyMOL allowing to map protein sector predictions on 3D structures.

The software is organized in different modules detailed below:

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Citing COCOA-Tree

If you use COCOA-Tree in a scientific publication, we would appreciate citations to the following paper:

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License information

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Copyright (c) 2025 The COCOA-Tree developers.
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