This project provides a solutions manual for all excercises in the two influential books on statistical molecular evolution by Ziheng Yang: Computational Molecular Evolution (CME) [Yang 2006] and Molecular Evolution: A Statistical Approach (MESA) [Yang 2014].

Authors: Sishuo Wang, Jianhao Lv (interestingly, Ziheng Yang and both authors are alumni of China Agricultural University)

• Sishuo Wang is from Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
• Jianhao Lv is from Nanfang College, Guangzhou, China.

We hope the solutions manual plays a tiny role in helping people better understand Ziheng's books and appreciate phylogenetics from a statistics perspective.

The solutions manual has NOT been formally reviewed, because everyone is welcome to review it. So by no means are the solutions to be taken as a “standard answer”. Instead, you are strongly encouraged to share your feedback and explore alternative solutions via this GitHub platform. Your contributions are important to help foster a community-driven effort to assist anyone interested in delving deeper into molecular evolution.

Notes

1. We aim to help biologists better understand computational molecular evolution by providing

   • very detailed step-by-step solutions
   • code as R as possible (as that's familiar to most biologists), from programming to calculus, linear algebra and statistical computation
   • where possible, alternative solutions and both analytical and simulation solutions.

2. The problems cover only a tip of the iceberg of the original books so it is always highly recommended to carefully read the original books.

3. Ziheng provided very insightful solututions to four problems of Yang 2006. For these problems, we try to provide different solutions where possible, as also indicated above.

4. This work has never received any fund. If you find this github repository helpful, please consider ★ it.

Citation

Wang Sishuo, Lv Jianhao, A Solutions Manual for The Exercises of Ziheng Yang's Computational Molecular Evolution, and Molecular Evolution: A Statistical Approach (2024).

Note that the solutions to a few in Chapter 7 of MESA2014 are yet to be uploaded to github.

Licence

The solutions are distributed under CC-BY 4.0.

All problem statements are restricted to Oxford Publisher.

Acknowledgements

We are particularly grateful for Ziheng for roviding so many interesting problems in his books, and for his encouragement during the process we worked on the solutions. A list of people to acknowledge is included under the folder "Notes/". Those problems that specifically need help or validation are listed there, too.

Contact

For any comments or error reports, please feel free to use github or contact Sishuo Wang at sishuowang{at}hotmail.ca.