Welcome

Here you can explore the concept of a genomic transmission graph for modelling parasite transmission dynamics and population genetics. This website accompanies a paper on this topic in BioRxiv (link TBD).

Before getting started, take a quick look at how to use this book as it contains worked examples with Python code that you can run in the cloud for yourself even if you are new to programming.

The sections aren’t strictly ordered but this is a logical sequence to work through the scientific concepts:

1. Underlying concepts

2. The basic model

   • Time to coalescence

   • Nucleotide diversity

   • Haplotype homozygosity

   • Identity by descent

3. Within-host diversity

   • Estimating the quantum of transmission

   • Hw - Hs relationship

   • Estimating the rate of superinfection

4. Migration and population structure

   • Creating a metapopulation

   • Creating a subpopulation

5. Modelling epidemiological scenarios

   • Time series analysis

   • Transient scenarios

   • Local outbreak

Most of the worked examples use the Python package coalestr which works like this:

1. First you create a Population

2. Then you run get_coalescent

3. Then you run get_diversity

4. You can create a subpopulation with migration from a metapopulation

5. To analyse a time series you specify observation times