Archaeogenetics: Topics and Reading Assignments

The course is organized around several projects, each on a different topic. Each project will occupy several weeks of class. Each topic will eventually have a "Howto" link, which contains detailed instructions.

The Bash shell

Many of the steps in the Howto documents use the Bash shell, a command-line interpreter that is widely used in computational genetics. It is available on MacOS through the "Terminal" application and on Windows through the Windows Subsystem for Linux. Anyone using Linux will be familiar with it already.

I won't try to teach you Bash, but you should familiarize yourself with the basic commands--"ls", "pwd", "cd", "rm", and "mkdir"--and also with bash pipes, and the redirection of input and output. As you read the Howto documents, you'll see other commands, such as "sed", "awk", "tr", and "xargs". I would encourage you to look these up as you encounter them, and figure out how each command in the Howto works.

Topics

History of population size in a single population

Writing your own coalescent simulation.

History of a subdivided population

Coalescent simulations using ms-prime.