Program Supplement to Genomic Analysis of Human Population Structure

Over the course of my PhD project, Genomic Analysis of Human Population Structure, I wrote over sixty short programs (or scripts) to supplement my research, including a program that can carry out a bootstrap sub-sampling procedure on genetic data. It is expected that the scripts created for this research will be of use to other people carrying out similar work, and they have been written with the expectation that the scripts will be adapted by other people in the future.

Most commonly, the purpose of these scripts is to convert data from one file format to another -- data is often received in different formats from different researchers, and will usually need to be converted into another format in order to work with a particular program. Scripts have also been written for producing many of the figures seen in my thesis, as well as simple summary statistics. Where more complex calculations (in an external program) have been
required to be done repeatedly, a script has been created to automate that process.

Documentation for programs developed over the course of this research project is found in the file 'programs.pdf'. This Zenodo repository also contains the source code for those programs.

The chapters are arranged by programming language (Perl, R, shell), and contain a summary of the types of programs written in that language, followed by more verbose information about the programs that were written.

Note: these scripts and programs are in the state they were when my PhD thesis was published. Some have been updated since, and have been added to my bioinformatics scripts repository. If there's an issue, check there first (and please tell me even if the problem is fixed, so I can make a note here of the known problems).