_toc.yml

format: jb-book
root: intro
parts:
- caption:
  chapters:
  - file: what_is
- caption: Tree sequence basics
  chapters:
  - file: terminology_and_concepts
  - file: getting_started
- caption: Statistics and Analysis
  chapters:
  - file: analysing_tree_sequences
  - file: analysing_trees
  - file: incremental_algorithms
  - file: counting_topologies
  - file: parallelization
- caption: Further tskit tutorials
  chapters:
  - file: tables_and_editing
  - file: simplification
  - file: viz
  - file: metadata
  - file: args
- caption: Simulation
  chapters:
  - file: simulation_overview
  - file: no_mutations
  - file: advanced_msprime
    sections:
    - file: demography
    - file: bottlenecks
    - file: introgression
  - file: completing_forward_sims
  - file: forward_sims
  - file: more_forward_sims
- caption: Other languages
  # TODO: add basic C and maybe Rust tutes
  chapters:
  - file: tskitr
- caption: Development
  # TODO This would be a great place to put the general tskit development
  # guidelines.
  chapters:
  - file: tutorial_development
- caption: Tskit for ...
  chapters:
  - file: popgen.md
  - file: phylogen.md