Introduction | A Brief Welcome | Immunology background | Overview of the code | Importing data | Processing the sequencing data | Installing and loading alphabetr | Formatting and inputting sequencing data for alphabetr | Simulating sequencing data | Running the code | Creating the clonal structure of the T cell population | Simulating a TCR sequencing experiment | Finding candidate pairs | Performing frequency estimation on these pairs | Discriminating beta-sharing and dual TCR-alpha clones | Final frequency estimation | Evaluation of results