Strom 3

A tutorial for building Bayesian phylogenetic software using C++

This tutorial teaches you how to create C++ software that performs Bayesian phylogenetic analyses. It was written primarily to help students in my laboratory to develop software that they can later modify for their own purposes, but I hope it is more broadly useful.

This is the third version of the tutorial. It differs from the second version in the order in which features are added, in adding invariable sites and codon models, and in allowing data partitioning.

Note: (Many more) bugs have been fixed! If you are in the middle of the tutorial now, I would advise that you replace your code for the step you are on with the source code files for that step from the repository. The easy way to do this is to visit the GitHub repository, ensure you are on the source branch (not the master branch), navigate to your current step in the steps directory, and find the source code files for that step in the src directory under that step. See the Version History section of the source branch README (specifically version 3.2) to see my notes on this update.

Begin Tutorial

Three versions of the tutorial are provided. The Mac and Windows versions use graphical IDEs (Integrated Development Environments). The Mac version uses the Xcode IDE, while the Windows version uses the Visual Studio IDE. The Linux version shows you how to build software on an Ubuntu system without using a graphical IDE using the meson/ninja approach. Get started using your platform of choice below:

Author

The tutorial was written by Paul O. Lewis. Please write to me at paul.lewis@uconn.edu if you find errors.

Funding

This tutorial was developed as a broader impact project associated with National Science Foundation grant DEB-1354146 (Estimating the Bayesian phylogenetic information content of systematic data, PI Paul O. Lewis).

Acknowledgements

If there is anything in this tutorial that is well-designed, it is due to the patience and generosity of the many great teachers, mentors, and colleagues who have helped me over the years. The person who taught me the most about phylogenetics and, particularly, how to program phylogenetics is David Swofford, who sets a very high standard for code quality that improves the ability of all of us who try to attain it.

Licence

The software that you will create falls under the permissive open-source MIT License.