TOPIC: Pop gene & comparative genomics
- A working Unix environment (though practice environments are available for lessons below)
- Experience with the command line
- Lesson 1: Comparative Genomics using dN/dS
- Lesson 2: An Extremely Brief Introduction to the McDonald-Kreitman Test for Selection
- Lesson 3: Phylogenetically-structured Data
Date posted: 12 May 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber and Dr. Jake L. Weissman
- Synonymous vs. nonsynonymous mutations:
- Estimating selection using dN/dS
- Limitations of dN/dS
Date posted: 12 May 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
- Introduction to PAML
- PAML programs
- Input and output files
- Making a codon alignment
- The codeml.ctl file
- Running codeml
Content | Video presentation |
Primary tools/programs used:
Date posted: 20 May 2020
Author(s): Dr. Jake L. Weissman
Instructor(s): Dr. Jake L. Weissman and Arkadiy Garber
- Why the MK-Test?
- Intuition behind the test
- Running the test on a large set of genes from Listeria monocytogenes
Slides | Tutorial | Video presentation
Date posted: 13 July 2020
Author(s): Dr. Jake L. Weissman
Instructor(s): Dr. Jake L. Weissman
- Between-species comparative studies
- Dealing with phylogenetic structure (detecting phylogenetic signal in traits, correcting for it with PGLS)
Slides | Tutorial | Video presentation
- Lots of tutorials, especially for SNP data: Population Genetics in R
- Again, another set of intro tutorials that look nice: Population genetics and genomics in R
- pegas
- popgenome
- For the MK test: iMKT
- Free: Population and Quantitative Genetics by Graham Coop
- Not Free (but very good, instructor's pick): Molecular Population Genetics by Matt Hahn
(there are many good/short popgen textbooks, e.g., by Gillespie, the two above are just two good ones with a nice focus on practical considerations)