Arrival: 19 July 2015
Departure: 30 July 2015
Institutional home pages
I have done an extensive update of the lecture slides on codon models for 2016. The update includes greater coverage of the mechanistic process of codon evolution (via the MutSel framework). Because there is now less detail about fitting codon models to real data, I have included links to the 2015 slides below; these slides provide more practical information about the powers and pitfalls of inference under codon models.
2016 Lecture slides, Part 1:
2016 Lecture slides, Part 2:
(last year's slides)
2015 Lecture slides, Part 1: PDF file1 (2 slides per page)
2015 Lecture slides, Part 2: PDF file2 (2 slides per page)
PAML lab Materials
The lab exercises (PAML demo) have been published to a small website (link below). The site contains some additional resources. Please note that presentations may change up until the moment the lecture or lab begins. I will post modified PDFs after each talk.
PAML demo: Link to a website
PAML demo slides: PDF file (2 slides per page)
If you have some experience with codon models, and want to try out a tutorial for more advanced materials then use the link below to download an archive for a complete different set of PAML activities. This tutorial focuses on detecting episodic protein evolution via Branch-Site Model A. The tutorial also includes activities about (i) detecting MLE instabilities, (ii) carrying out robustness analyses, and (iii) use of smoothed bootstrap aggregation (SBA). The protocols for each activity are presented in UNIT XX of Protocols in Bioinformatics. The included PDF file for UNIT XX also includes recommendations for best practices when carrying out a large scale evolutionary survey for episodic adaptive evolution by using PAML.
Advanced PAML demo: