Test TreeSequences with different mutation rates

Test TreeSequences with different mutation rates#

Load a tree sequence object and try to change the mutation rate.

import numpy as np
import msprime
import tskit

from tskitetude import get_data_dir

Now load the tree sequence file generated with msprime

tsm100M300I = tskit.load(get_data_dir() / "sheepTSsimMilano/tsm100M300I.trees")
tsm100M300I

Tree Sequence
Trees	2 695 768
Sequence Length	1e+08
Time Units	generations
Sample Nodes	4 810
Total Size	536.2 MiB
Metadata	No Metadata

Table	Rows	Size	Has Metadata
Edges	10 271 864	313.5 MiB
Individuals	2 405	65.8 KiB
Migrations	0	8 Bytes
Mutations	1 727 679	61.0 MiB
Nodes	1 590 538	42.5 MiB
Populations	18	880 Bytes	✅
Provenances	2	6.9 KiB
Sites	1 712 620	40.8 MiB

Provenance Timestamp	Software Name	Version	Command	Full record
11 September, 2024 at 07:03:07 AM	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: 5.87e-09 model: None start_time: None end_time: None discrete_genome: None keep: None random_seed: 13 environment: dict os: dict system: Linux node: node2i15.ecdf.ed.ac.uk release: 3.10.0-1160.108.1.el7.x86_64 version: #1 SMP Wed Jan 24 08:37:16 CST 2024 machine: x86_64 python: dict implementation: CPython version: 3.8.13 libraries: dict kastore: dict version: 2.1.1 tskit: dict version: 0.5.2 gsl: dict version: 2.6
11 September, 2024 at 07:03:00 AM	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: dict MM: 5 II: 300 A: 300 B: 300 C: 300 D: 300 E: 300 F: 300 G: 300 demography: dict populations: list dict initial_size: 76000 growth_rate: 0 name: MManc description: extra_metadata: dict default_sampling_time: 5000 initially_active: False id: 0 dict initial_size: 76000 growth_rate: 0 name: MM description: extra_metadata: dict default_sampling_time: None initially_active: None id: 1 dict initial_size: 170000 growth_rate: 0 name: IIanc description: extra_metadata: dict default_sampling_time: 3000 initially_active: False id: 2 dict initial_size: 170000 growth_rate: 0 name: II description: extra_metadata: dict default_sampling_time: None initially_active: None id: 3 dict initial_size: 850 growth_rate: 0 name: Aanc description: extra_metadata: dict default_sampling_time: 1500 initially_active: False id: 4 dict initial_size: 850 growth_rate: 0 name: A description: extra_metadata: dict default_sampling_time: None initially_active: None id: 5 dict initial_size: 850 growth_rate: 0 name: Banc description: extra_metadata: dict default_sampling_time: 750 initially_active: False id: 6 dict initial_size: 850 growth_rate: 0 name: B description: extra_metadata: dict default_sampling_time: None initially_active: None id: 7 dict initial_size: 850 growth_rate: 0 name: Canc description: extra_metadata: dict default_sampling_time: 375 initially_active: False id: 8 dict initial_size: 850 growth_rate: 0 name: C description: extra_metadata: dict default_sampling_time: None initially_active: None id: 9 dict initial_size: 850 growth_rate: 0 name: Danc description: extra_metadata: dict default_sampling_time: 188 initially_active: False id: 10 dict initial_size: 850 growth_rate: 0 name: D description: extra_metadata: dict default_sampling_time: None initially_active: None id: 11 dict initial_size: 850 growth_rate: 0 name: Eanc description: extra_metadata: dict default_sampling_time: 94 initially_active: False id: 12 dict initial_size: 850 growth_rate: 0 name: E description: extra_metadata: dict default_sampling_time: None initially_active: None id: 13 dict initial_size: 850 growth_rate: 0 name: Fanc description: extra_metadata: dict default_sampling_time: 47 initially_active: False id: 14 dict initial_size: 850 growth_rate: 0 name: F description: extra_metadata: dict default_sampling_time: None initially_active: None id: 15 dict initial_size: 850 growth_rate: 0 name: Ganc description: extra_metadata: dict default_sampling_time: None initially_active: None id: 16 dict initial_size: 850 growth_rate: 0 name: G description: extra_metadata: dict default_sampling_time: None initially_active: None id: 17 events: list dict time: 47 derived: list F G ancestral: Fanc dict time: 94 derived: list Fanc E ancestral: Eanc dict time: 188 derived: list Eanc D ancestral: Danc dict time: 375 derived: list Danc C ancestral: Canc dict time: 750 derived: list Canc B ancestral: Banc dict time: 1500 derived: list Banc A ancestral: Aanc dict time: 3000 derived: list Aanc II ancestral: IIanc dict time: 5000 derived: list IIanc MM ancestral: MManc migration_matrix: list list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 __class__: msprime.demography.Demography sequence_length: 100000000 discrete_genome: None recombination_rate: 1e-08 gene_conversion_rate: None gene_conversion_tract_length: None population_size: None ploidy: None model: list dict duration: 500 __class__: msprime.ancestry.DiscreteTimeW rightFisher dict duration: None __class__: msprime.ancestry.StandardCoale scent initial_state: None start_time: None end_time: None record_migrations: None record_full_arg: None num_labels: None random_seed: 12 replicate_index: 0 environment: dict os: dict system: Linux node: node2i15.ecdf.ed.ac.uk release: 3.10.0-1160.108.1.el7.x86_64 version: #1 SMP Wed Jan 24 08:37:16 CST 2024 machine: x86_64 python: dict implementation: CPython version: 3.8.13 libraries: dict kastore: dict version: 2.1.1 tskit: dict version: 0.5.2 gsl: dict version: 2.6

To cite this software, please consult the citation manual: https://tskit.dev/citation/

cut first 1MB from the treesequence object: remember to trim the right sequence (with no data)

intervals = np.array([[1, 1_000_000]])
tsm1M300I = tsm100M300I.keep_intervals(intervals).rtrim()
tsm1M300I

Tree Sequence
Trees	27 108
Sequence Length	1 000 000
Time Units	generations
Sample Nodes	4 810
Total Size	6.1 MiB
Metadata	No Metadata

Table	Rows	Size	Has Metadata
Edges	112 392	3.4 MiB
Individuals	2 405	65.8 KiB
Migrations	0	8 Bytes
Mutations	17 099	617.9 KiB
Nodes	26 740	731.2 KiB
Populations	17	840 Bytes	✅
Provenances	4	7.8 KiB
Sites	16 954	413.9 KiB

Provenance Timestamp	Software Name	Version	Command	Full record
19 December, 2025 at 01:36:25 PM	tskit	1.0.0b3	rtrim	Details dict schema_version: 1.0.0 software: dict name: tskit version: 1.0.0b3 parameters: dict command: rtrim environment: dict os: dict system: Linux node: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64 python: dict implementation: CPython version: 3.12.12 libraries: dict kastore: dict version: 2.1.1
19 December, 2025 at 01:36:25 PM	tskit	1.0.0b3	keep_intervals	Details dict schema_version: 1.0.0 software: dict name: tskit version: 1.0.0b3 parameters: dict command: keep_intervals TODO: add parameters environment: dict os: dict system: Linux node: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64 python: dict implementation: CPython version: 3.12.12 libraries: dict kastore: dict version: 2.1.1
11 September, 2024 at 07:03:07 AM	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: 5.87e-09 model: None start_time: None end_time: None discrete_genome: None keep: None random_seed: 13 environment: dict os: dict system: Linux node: node2i15.ecdf.ed.ac.uk release: 3.10.0-1160.108.1.el7.x86_64 version: #1 SMP Wed Jan 24 08:37:16 CST 2024 machine: x86_64 python: dict implementation: CPython version: 3.8.13 libraries: dict kastore: dict version: 2.1.1 tskit: dict version: 0.5.2 gsl: dict version: 2.6
11 September, 2024 at 07:03:00 AM	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: dict MM: 5 II: 300 A: 300 B: 300 C: 300 D: 300 E: 300 F: 300 G: 300 demography: dict populations: list dict initial_size: 76000 growth_rate: 0 name: MManc description: extra_metadata: dict default_sampling_time: 5000 initially_active: False id: 0 dict initial_size: 76000 growth_rate: 0 name: MM description: extra_metadata: dict default_sampling_time: None initially_active: None id: 1 dict initial_size: 170000 growth_rate: 0 name: IIanc description: extra_metadata: dict default_sampling_time: 3000 initially_active: False id: 2 dict initial_size: 170000 growth_rate: 0 name: II description: extra_metadata: dict default_sampling_time: None initially_active: None id: 3 dict initial_size: 850 growth_rate: 0 name: Aanc description: extra_metadata: dict default_sampling_time: 1500 initially_active: False id: 4 dict initial_size: 850 growth_rate: 0 name: A description: extra_metadata: dict default_sampling_time: None initially_active: None id: 5 dict initial_size: 850 growth_rate: 0 name: Banc description: extra_metadata: dict default_sampling_time: 750 initially_active: False id: 6 dict initial_size: 850 growth_rate: 0 name: B description: extra_metadata: dict default_sampling_time: None initially_active: None id: 7 dict initial_size: 850 growth_rate: 0 name: Canc description: extra_metadata: dict default_sampling_time: 375 initially_active: False id: 8 dict initial_size: 850 growth_rate: 0 name: C description: extra_metadata: dict default_sampling_time: None initially_active: None id: 9 dict initial_size: 850 growth_rate: 0 name: Danc description: extra_metadata: dict default_sampling_time: 188 initially_active: False id: 10 dict initial_size: 850 growth_rate: 0 name: D description: extra_metadata: dict default_sampling_time: None initially_active: None id: 11 dict initial_size: 850 growth_rate: 0 name: Eanc description: extra_metadata: dict default_sampling_time: 94 initially_active: False id: 12 dict initial_size: 850 growth_rate: 0 name: E description: extra_metadata: dict default_sampling_time: None initially_active: None id: 13 dict initial_size: 850 growth_rate: 0 name: Fanc description: extra_metadata: dict default_sampling_time: 47 initially_active: False id: 14 dict initial_size: 850 growth_rate: 0 name: F description: extra_metadata: dict default_sampling_time: None initially_active: None id: 15 dict initial_size: 850 growth_rate: 0 name: Ganc description: extra_metadata: dict default_sampling_time: None initially_active: None id: 16 dict initial_size: 850 growth_rate: 0 name: G description: extra_metadata: dict default_sampling_time: None initially_active: None id: 17 events: list dict time: 47 derived: list F G ancestral: Fanc dict time: 94 derived: list Fanc E ancestral: Eanc dict time: 188 derived: list Eanc D ancestral: Danc dict time: 375 derived: list Danc C ancestral: Canc dict time: 750 derived: list Canc B ancestral: Banc dict time: 1500 derived: list Banc A ancestral: Aanc dict time: 3000 derived: list Aanc II ancestral: IIanc dict time: 5000 derived: list IIanc MM ancestral: MManc migration_matrix: list list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 __class__: msprime.demography.Demography sequence_length: 100000000 discrete_genome: None recombination_rate: 1e-08 gene_conversion_rate: None gene_conversion_tract_length: None population_size: None ploidy: None model: list dict duration: 500 __class__: msprime.ancestry.DiscreteTimeW rightFisher dict duration: None __class__: msprime.ancestry.StandardCoale scent initial_state: None start_time: None end_time: None record_migrations: None record_full_arg: None num_labels: None random_seed: 12 replicate_index: 0 environment: dict os: dict system: Linux node: node2i15.ecdf.ed.ac.uk release: 3.10.0-1160.108.1.el7.x86_64 version: #1 SMP Wed Jan 24 08:37:16 CST 2024 machine: x86_64 python: dict implementation: CPython version: 3.8.13 libraries: dict kastore: dict version: 2.1.1 tskit: dict version: 0.5.2 gsl: dict version: 2.6

To cite this software, please consult the citation manual: https://tskit.dev/citation/

n_mutations = sum(1 for m in tsm1M300I.mutations())
print(f"Number of mutations in tsm1M300I: {n_mutations}")

Number of mutations in tsm1M300I: 17099

Attempt to remove the mutations: collect the tables, remove mutations and generate a new tree sequence:

tables = tsm1M300I.dump_tables()
tables.mutations.clear()
tsm1M300I_no_mutations = tables.tree_sequence()
tsm1M300I_no_mutations

Tree Sequence
Trees	27 108
Sequence Length	1 000 000
Time Units	generations
Sample Nodes	4 810
Total Size	5.5 MiB
Metadata	No Metadata

Table	Rows	Size	Has Metadata
Edges	112 392	3.4 MiB
Individuals	2 405	65.8 KiB
Migrations	0	8 Bytes
Mutations	0	16 Bytes
Nodes	26 740	731.2 KiB
Populations	17	840 Bytes	✅
Provenances	4	7.8 KiB
Sites	16 954	413.9 KiB

Provenance Timestamp	Software Name	Version	Command	Full record
19 December, 2025 at 01:36:25 PM	tskit	1.0.0b3	rtrim	Details dict schema_version: 1.0.0 software: dict name: tskit version: 1.0.0b3 parameters: dict command: rtrim environment: dict os: dict system: Linux node: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64 python: dict implementation: CPython version: 3.12.12 libraries: dict kastore: dict version: 2.1.1
19 December, 2025 at 01:36:25 PM	tskit	1.0.0b3	keep_intervals	Details dict schema_version: 1.0.0 software: dict name: tskit version: 1.0.0b3 parameters: dict command: keep_intervals TODO: add parameters environment: dict os: dict system: Linux node: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64 python: dict implementation: CPython version: 3.12.12 libraries: dict kastore: dict version: 2.1.1
11 September, 2024 at 07:03:07 AM	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: 5.87e-09 model: None start_time: None end_time: None discrete_genome: None keep: None random_seed: 13 environment: dict os: dict system: Linux node: node2i15.ecdf.ed.ac.uk release: 3.10.0-1160.108.1.el7.x86_64 version: #1 SMP Wed Jan 24 08:37:16 CST 2024 machine: x86_64 python: dict implementation: CPython version: 3.8.13 libraries: dict kastore: dict version: 2.1.1 tskit: dict version: 0.5.2 gsl: dict version: 2.6
11 September, 2024 at 07:03:00 AM	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: dict MM: 5 II: 300 A: 300 B: 300 C: 300 D: 300 E: 300 F: 300 G: 300 demography: dict populations: list dict initial_size: 76000 growth_rate: 0 name: MManc description: extra_metadata: dict default_sampling_time: 5000 initially_active: False id: 0 dict initial_size: 76000 growth_rate: 0 name: MM description: extra_metadata: dict default_sampling_time: None initially_active: None id: 1 dict initial_size: 170000 growth_rate: 0 name: IIanc description: extra_metadata: dict default_sampling_time: 3000 initially_active: False id: 2 dict initial_size: 170000 growth_rate: 0 name: II description: extra_metadata: dict default_sampling_time: None initially_active: None id: 3 dict initial_size: 850 growth_rate: 0 name: Aanc description: extra_metadata: dict default_sampling_time: 1500 initially_active: False id: 4 dict initial_size: 850 growth_rate: 0 name: A description: extra_metadata: dict default_sampling_time: None initially_active: None id: 5 dict initial_size: 850 growth_rate: 0 name: Banc description: extra_metadata: dict default_sampling_time: 750 initially_active: False id: 6 dict initial_size: 850 growth_rate: 0 name: B description: extra_metadata: dict default_sampling_time: None initially_active: None id: 7 dict initial_size: 850 growth_rate: 0 name: Canc description: extra_metadata: dict default_sampling_time: 375 initially_active: False id: 8 dict initial_size: 850 growth_rate: 0 name: C description: extra_metadata: dict default_sampling_time: None initially_active: None id: 9 dict initial_size: 850 growth_rate: 0 name: Danc description: extra_metadata: dict default_sampling_time: 188 initially_active: False id: 10 dict initial_size: 850 growth_rate: 0 name: D description: extra_metadata: dict default_sampling_time: None initially_active: None id: 11 dict initial_size: 850 growth_rate: 0 name: Eanc description: extra_metadata: dict default_sampling_time: 94 initially_active: False id: 12 dict initial_size: 850 growth_rate: 0 name: E description: extra_metadata: dict default_sampling_time: None initially_active: None id: 13 dict initial_size: 850 growth_rate: 0 name: Fanc description: extra_metadata: dict default_sampling_time: 47 initially_active: False id: 14 dict initial_size: 850 growth_rate: 0 name: F description: extra_metadata: dict default_sampling_time: None initially_active: None id: 15 dict initial_size: 850 growth_rate: 0 name: Ganc description: extra_metadata: dict default_sampling_time: None initially_active: None id: 16 dict initial_size: 850 growth_rate: 0 name: G description: extra_metadata: dict default_sampling_time: None initially_active: None id: 17 events: list dict time: 47 derived: list F G ancestral: Fanc dict time: 94 derived: list Fanc E ancestral: Eanc dict time: 188 derived: list Eanc D ancestral: Danc dict time: 375 derived: list Danc C ancestral: Canc dict time: 750 derived: list Canc B ancestral: Banc dict time: 1500 derived: list Banc A ancestral: Aanc dict time: 3000 derived: list Aanc II ancestral: IIanc dict time: 5000 derived: list IIanc MM ancestral: MManc migration_matrix: list list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 __class__: msprime.demography.Demography sequence_length: 100000000 discrete_genome: None recombination_rate: 1e-08 gene_conversion_rate: None gene_conversion_tract_length: None population_size: None ploidy: None model: list dict duration: 500 __class__: msprime.ancestry.DiscreteTimeW rightFisher dict duration: None __class__: msprime.ancestry.StandardCoale scent initial_state: None start_time: None end_time: None record_migrations: None record_full_arg: None num_labels: None random_seed: 12 replicate_index: 0 environment: dict os: dict system: Linux node: node2i15.ecdf.ed.ac.uk release: 3.10.0-1160.108.1.el7.x86_64 version: #1 SMP Wed Jan 24 08:37:16 CST 2024 machine: x86_64 python: dict implementation: CPython version: 3.8.13 libraries: dict kastore: dict version: 2.1.1 tskit: dict version: 0.5.2 gsl: dict version: 2.6

To cite this software, please consult the citation manual: https://tskit.dev/citation/

Now generate TS objects with mutations:

mu = 5.87e-9
mutations = [0.1, 0.5, 2, 10]
mutation_rates = [mutation * mu for mutation in mutations]

def simulate_mutations(ts, mutation_rate):
    return(msprime.sim_mutations(ts, rate=mutation_rate, random_seed=42))

simulated_trees = [simulate_mutations(tsm1M300I_no_mutations, mutation_rate) for mutation_rate in mutation_rates]

inspect a simulated tree:

simulated_trees[0]

Tree Sequence
Trees	27 108
Sequence Length	1 000 000
Time Units	generations
Sample Nodes	4 810
Total Size	5.6 MiB
Metadata	No Metadata

Table	Rows	Size	Has Metadata
Edges	112 392	3.4 MiB
Individuals	2 405	65.8 KiB
Migrations	0	8 Bytes
Mutations	1 737	62.8 KiB
Nodes	26 740	731.2 KiB
Populations	17	840 Bytes	✅
Provenances	5	8.5 KiB
Sites	18 659	455.6 KiB

Provenance Timestamp	Software Name	Version	Command	Full record
19 December, 2025 at 01:36:25 PM	msprime	1.3.4	sim_mutations	Details dict schema_version: 1.0.0 software: dict name: msprime version: 1.3.4 parameters: dict command: sim_mutations tree_sequence: dict __constant__: __current_ts__ rate: 5.87e-10 model: None start_time: None end_time: None discrete_genome: None keep: None random_seed: 42 environment: dict os: dict system: Linux node: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64 python: dict implementation: CPython version: 3.12.12 libraries: dict kastore: dict version: 2.1.1 tskit: dict version: 1.0.0b3 gsl: dict version: 2.6
19 December, 2025 at 01:36:25 PM	tskit	1.0.0b3	rtrim	Details dict schema_version: 1.0.0 software: dict name: tskit version: 1.0.0b3 parameters: dict command: rtrim environment: dict os: dict system: Linux node: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64 python: dict implementation: CPython version: 3.12.12 libraries: dict kastore: dict version: 2.1.1
19 December, 2025 at 01:36:25 PM	tskit	1.0.0b3	keep_intervals	Details dict schema_version: 1.0.0 software: dict name: tskit version: 1.0.0b3 parameters: dict command: keep_intervals TODO: add parameters environment: dict os: dict system: Linux node: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64 python: dict implementation: CPython version: 3.12.12 libraries: dict kastore: dict version: 2.1.1
11 September, 2024 at 07:03:07 AM	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: 5.87e-09 model: None start_time: None end_time: None discrete_genome: None keep: None random_seed: 13 environment: dict os: dict system: Linux node: node2i15.ecdf.ed.ac.uk release: 3.10.0-1160.108.1.el7.x86_64 version: #1 SMP Wed Jan 24 08:37:16 CST 2024 machine: x86_64 python: dict implementation: CPython version: 3.8.13 libraries: dict kastore: dict version: 2.1.1 tskit: dict version: 0.5.2 gsl: dict version: 2.6
11 September, 2024 at 07:03:00 AM	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: dict MM: 5 II: 300 A: 300 B: 300 C: 300 D: 300 E: 300 F: 300 G: 300 demography: dict populations: list dict initial_size: 76000 growth_rate: 0 name: MManc description: extra_metadata: dict default_sampling_time: 5000 initially_active: False id: 0 dict initial_size: 76000 growth_rate: 0 name: MM description: extra_metadata: dict default_sampling_time: None initially_active: None id: 1 dict initial_size: 170000 growth_rate: 0 name: IIanc description: extra_metadata: dict default_sampling_time: 3000 initially_active: False id: 2 dict initial_size: 170000 growth_rate: 0 name: II description: extra_metadata: dict default_sampling_time: None initially_active: None id: 3 dict initial_size: 850 growth_rate: 0 name: Aanc description: extra_metadata: dict default_sampling_time: 1500 initially_active: False id: 4 dict initial_size: 850 growth_rate: 0 name: A description: extra_metadata: dict default_sampling_time: None initially_active: None id: 5 dict initial_size: 850 growth_rate: 0 name: Banc description: extra_metadata: dict default_sampling_time: 750 initially_active: False id: 6 dict initial_size: 850 growth_rate: 0 name: B description: extra_metadata: dict default_sampling_time: None initially_active: None id: 7 dict initial_size: 850 growth_rate: 0 name: Canc description: extra_metadata: dict default_sampling_time: 375 initially_active: False id: 8 dict initial_size: 850 growth_rate: 0 name: C description: extra_metadata: dict default_sampling_time: None initially_active: None id: 9 dict initial_size: 850 growth_rate: 0 name: Danc description: extra_metadata: dict default_sampling_time: 188 initially_active: False id: 10 dict initial_size: 850 growth_rate: 0 name: D description: extra_metadata: dict default_sampling_time: None initially_active: None id: 11 dict initial_size: 850 growth_rate: 0 name: Eanc description: extra_metadata: dict default_sampling_time: 94 initially_active: False id: 12 dict initial_size: 850 growth_rate: 0 name: E description: extra_metadata: dict default_sampling_time: None initially_active: None id: 13 dict initial_size: 850 growth_rate: 0 name: Fanc description: extra_metadata: dict default_sampling_time: 47 initially_active: False id: 14 dict initial_size: 850 growth_rate: 0 name: F description: extra_metadata: dict default_sampling_time: None initially_active: None id: 15 dict initial_size: 850 growth_rate: 0 name: Ganc description: extra_metadata: dict default_sampling_time: None initially_active: None id: 16 dict initial_size: 850 growth_rate: 0 name: G description: extra_metadata: dict default_sampling_time: None initially_active: None id: 17 events: list dict time: 47 derived: list F G ancestral: Fanc dict time: 94 derived: list Fanc E ancestral: Eanc dict time: 188 derived: list Eanc D ancestral: Danc dict time: 375 derived: list Danc C ancestral: Canc dict time: 750 derived: list Canc B ancestral: Banc dict time: 1500 derived: list Banc A ancestral: Aanc dict time: 3000 derived: list Aanc II ancestral: IIanc dict time: 5000 derived: list IIanc MM ancestral: MManc migration_matrix: list list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 list 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 __class__: msprime.demography.Demography sequence_length: 100000000 discrete_genome: None recombination_rate: 1e-08 gene_conversion_rate: None gene_conversion_tract_length: None population_size: None ploidy: None model: list dict duration: 500 __class__: msprime.ancestry.DiscreteTimeW rightFisher dict duration: None __class__: msprime.ancestry.StandardCoale scent initial_state: None start_time: None end_time: None record_migrations: None record_full_arg: None num_labels: None random_seed: 12 replicate_index: 0 environment: dict os: dict system: Linux node: node2i15.ecdf.ed.ac.uk release: 3.10.0-1160.108.1.el7.x86_64 version: #1 SMP Wed Jan 24 08:37:16 CST 2024 machine: x86_64 python: dict implementation: CPython version: 3.8.13 libraries: dict kastore: dict version: 2.1.1 tskit: dict version: 0.5.2 gsl: dict version: 2.6

To cite this software, please consult the citation manual: https://tskit.dev/citation/

for idx, ts in enumerate(simulated_trees):
    outfile = get_data_dir() / "sheepTSsimMilano" / f"tsm1M300I_{mutations[idx]}mu.trees"
    ts.dump(outfile)
    print(f"Dumped {outfile}")

Dumped /home/core/TSKITetude/data/sheepTSsimMilano/tsm1M300I_0.1mu.trees
Dumped /home/core/TSKITetude/data/sheepTSsimMilano/tsm1M300I_0.5mu.trees
Dumped /home/core/TSKITetude/data/sheepTSsimMilano/tsm1M300I_2mu.trees

Dumped /home/core/TSKITetude/data/sheepTSsimMilano/tsm1M300I_10mu.trees