msprime

library1.4.2pypypi✓ verified 79d ago

msprime is a fast, scalable Python library for simulating genealogical trees and genomic sequence data under population genetic models using the coalescent with recombination. Current version 1.4.1 supports Python >=3.11. Released under GPL, maintained by the TSKIT team with regular updates.

data ai-ml

pip install msprime

github ↗package ↗homepage ↗docs ↗changelog ↗

INSTALL

IMPORT

SIG · MSPRIME

msprime

datapythonv1.4.2

Install

5.4s avg

Import

862ms

Disk

110MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.4.0 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

build_error

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 5.4s · import 0.862s · 116MB

110MB installed

● package 110MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

simulate

✓ from msprime import simulate

✗ import msprime as ms

AncestryModel

✓ from msprime import AncestryModel

Demography

✓ from msprime import Demography

Simulate a basic coalescent tree sequence with recombination.

import msprime # Simulate a coalescent sample of 10 chromosomes recombination_rate = 1e-8 sequence_length = 1e4 ts = msprime.simulate( sample_size=10, recombination_rate=recombination_rate, length=sequence_length, random_seed=42 ) print(ts.num_trees, ts.num_samples)

msp --version

Debug

Known issues

breakingIn msprime 1.0, the API was overhauled: `msprime.simulate()` replaces `msprime.simulate()` from older versions (no change in name but parameter changes). The `Ne` parameter is no longer accepted; use `population_size`.

fix

Replace `Ne=X` with `population_size=X`. Ensure you use msprime 1.x imports.

affects: >=0.7.0, <1.0

deprecated`msprime.simulate()` with mutation_rate parameter is deprecated in favor of `msprime.mutate()` applied to a tree sequence.

fix

Run `ts = msprime.simulate(...)` then `ts = msprime.mutate(ts, rate=1e-8)`. See docs for details.

affects: >=1.0

gotchaSetting `random_seed` to the same value will produce identical results. For parallel simulations, ensure each process uses a unique seed.

fix

Use different seeds (e.g., derived from process ID) when running parallel simulations.

affects: all

gotchaWhen using `msprime.simulate()` with multiple populations, the `sample_size` parameter expects a list of sample sizes per population, not the total. Incorrect usage leads to confusing errors.

fix

Pass a list: `sample_size=[5,5]` for two populations. Do not pass total 10.

affects: >=1.0

breakingSupport for Python 3.8 and 3.9 dropped in msprime 1.4.0. Requires Python >=3.11 as of 1.4.1.

fix

Upgrade Python to 3.11 or later.

affects: >=1.4.0

Upgrade

Version history

1.4.2latest on PyPI · released May 20, 2026

Audit

Dependencies

numpyrequiredRequired for numerical operations.

tskitrequiredRequired for tree sequence data structures and analysis.

Agent activity

4 hits · last 30 days

node

Resources

githubhttps://github.com/tskit-dev/msprime ↗

packagehttps://pypi.org/project/msprime/ ↗

homepagehttps://tskit.dev/msprime ↗

docshttps://tskit.dev/msprime/docs/stable ↗

changeloghttps://tskit.dev/msprime/docs/stable/CHANGELOG.html ↗