The manual is divided into the following pages:

  * [Installation](install.md)
  * [Quick start](quick-start.md)
  * [Subcommands](subcommands.md)
  * [Paired loci](paired-loci.md)
  * [Output formats](output-formats.md)
  * [Plotting](plotting.md)
  * [Germline inference confidence](germline-inference.md)
  * [Parallelization](parallel.md)
