Quickstart

Our tutorials site has a more extensive tutorial on Getting started with tskit. Below we just give a quick flavour of the Python API (note that APIs in C and Rust exist, and it is also possible to interface to the Python library in R).

Basic properties

Any tree sequence, such as one generated by msprime, can be loaded, and a summary table printed. This example uses a small tree sequence, but the tskit library scales effectively to ones encoding millions of genomes and variable sites.

import tskit

ts = tskit.load("data/basic_tree_seq.trees")  # Or generate using e.g. msprime.sim_ancestry()
ts  # In a Jupyter notebook this displays a summary table. Otherwise use print(ts)

Tree Sequence
Trees	4
Sequence Length	10,000.0
Time Units	generations
Sample Nodes	6
Total Size	3.5 KiB
Metadata	No Metadata

Table	Rows	Size	Has Metadata
Edges	20	648 Bytes
Individuals	3	108 Bytes
Migrations	0	8 Bytes
Mutations	5	201 Bytes
Nodes	14	400 Bytes
Populations	1	224 Bytes	✅
Provenances	2	1.7 KiB
Sites	5	141 Bytes

Provenance Timestamp	Software Name	Version	Command	Full record
14 July, 2022 at 09:51:11 PM	msprime	1.2.0	sim_mutations	Details dict schema_version: 1.0.0 software: dict name: msprime version: 1.2.0 parameters: dict command: sim_mutations tree_sequence: dict __constant__: __current_ts__ rate: 2e-07 model: None start_time: None end_time: None discrete_genome: None keep: None random_seed: 123 environment: dict os: dict system: Darwin node: Yans-New-Air release: 20.6.0 version: Darwin Kernel Version 20.6.0:<br/>Tue Feb 22 21:10:41 PST 2022; <br/>root:xnu-<br/>7195.141.26~1/RELEASE_X86_64 machine: x86_64 python: dict implementation: CPython version: 3.9.10 libraries: dict kastore: dict version: 2.1.1 tskit: dict version: 0.5.1 gsl: dict version: 2.7
14 July, 2022 at 09:51:11 PM	msprime	1.2.0	sim_ancestry	Details dict schema_version: 1.0.0 software: dict name: msprime version: 1.2.0 parameters: dict command: sim_ancestry samples: 3 demography: None sequence_length: 10000.0 discrete_genome: None recombination_rate: 1e-07 gene_conversion_rate: None gene_conversion_tract_length: None population_size: 1000 ploidy: None model: dtwf initial_state: None start_time: None end_time: None record_migrations: None record_full_arg: None num_labels: None random_seed: 665 replicate_index: 0 environment: dict os: dict system: Darwin node: Yans-New-Air release: 20.6.0 version: Darwin Kernel Version 20.6.0:<br/>Tue Feb 22 21:10:41 PST 2022; <br/>root:xnu-<br/>7195.141.26~1/RELEASE_X86_64 machine: x86_64 python: dict implementation: CPython version: 3.9.10 libraries: dict kastore: dict version: 2.1.1 tskit: dict version: 0.5.1 gsl: dict version: 2.7

Individual trees

You can get e.g. the first tree in the tree sequence and analyse it.

first_tree = ts.first()
print("Total branch length in first tree is", first_tree.total_branch_length, ts.time_units)
print("The first of", ts.num_trees, "trees is plotted below")
first_tree.draw_svg(y_axis=True)  # plot the tree: only useful for small trees

Total branch length in first tree is 4496.0 generations
The first of 4 trees is plotted below

Extracting genetic data

A tree sequence provides an extremely compact way to store genetic variation data. The trees allow this data to be decoded at each site:

for variant in ts.variants():
    print(
        "Variable site", variant.site.id,
        "at genome position", variant.site.position,
        ":", [variant.alleles[g] for g in variant.genotypes],
    )

Variable site 0 at genome position 536.0 : ['A', 'A', 'A', 'A', 'G', 'A']
Variable site 1 at genome position 2447.0 : ['C', 'G', 'G', 'G', 'G', 'G']
Variable site 2 at genome position 6947.0 : ['G', 'C', 'C', 'C', 'C', 'C']
Variable site 3 at genome position 7868.0 : ['C', 'C', 'C', 'C', 'C', 'T']
Variable site 4 at genome position 8268.0 : ['C', 'C', 'C', 'C', 'T', 'C']

Analysis

Tree sequences enable efficient analysis of genetic variation using a comprehensive range of built-in Statistics:

genetic_diversity = ts.diversity()
print("Av. genetic diversity across the genome is", genetic_diversity)

branch_diversity = ts.diversity(mode="branch")
print("Av. genealogical dist. between pairs of tips is", branch_diversity,  ts.time_units)

Av. genetic diversity across the genome is 0.00016666666666666666
Av. genealogical dist. between pairs of tips is 1645.8752266666668 generations

Plotting the whole tree sequence

This can give you a visual feel for small genealogies:

ts.draw_svg(
    size=(800, 300),
    y_axis=True,
    mutation_labels={m.id: m.derived_state for m in ts.mutations()},
)

Underlying data structures

The data that defines a tree sequence is stored in a set of tables. These tables can be viewed, and copies of the tables can be edited to create a new tree sequence.

# The sites table is one of several tables that underlie a tree sequence
ts.tables.sites

id	position	ancestral_state	metadata
0	536	A
1	2,447	G
2	6,947	C
3	7,868	C
4	8,268	C

The rest of this documentation gives a comprehensive description of the entire tskit library, including descriptions and definitions of all the tables.