How to make a dataset for phylogeny and the background of mathematical theory

Molecular phylogenetic analysis is a very important method of analysis for understanding the evolution of organisms and so on. The method of molecular phylogenetic analysis itself is often discussed, and you are probably familiar with the background of the analysis. The dataset to be analyzed is just as important as the analysis method. However, it is not well known how the data set is made and what the methodology behind it is. Therefore, I will outline the background to the creation of data sets.