ZOMBI2 ZOMBI2 logo

🌐 Website · Gallery · Documentation · Manual (pdf)

CI PyPI Docs License: MIT Python 3.10+

Simulating the evolution of species, genomes, sequences and traits.

ZOMBI2 simulates evolution at four levels: the species tree of lineages, the genomes that evolve along it, the sequences inside each gene, and the traits a lineage carries. Use it to generate benchmark datasets with known ground truth for phylogenetic and comparative methods.

Install

pip install zombi2

Quickstart

zombi2 species   out/ --birth 1 --death 0.3 --n-extant 20 --seed 1
zombi2 genomes   out/ --duplication 0.2 --transfer 0.1 --loss 0.25 --seed 1
zombi2 sequences out/ --model hky85 --length 1000 --divergence 0.2 --seed 1

From Python, each level is one function, and the result object carries the history:

from zombi2 import species, genomes, sequences
from zombi2.sequences.substitution_models import hky85

sp = species.simulate_species_tree(birth=1.0, death=0.3, n_extant=20, seed=1)
g  = genomes.simulate_genomes_family(sp, duplication=0.2, transfer=0.1, loss=0.25, seed=1)
s  = sequences.simulate_sequences(g, model=hky85(), length=1000, divergence=0.2, seed=1)

g.gene_trees                    # the true gene tree of every family

sp.write("out/")                # the trees, the event log and the fates
g.write("out/")                 # gene trees, the event log, profiles
s.write("out/")                 # alignments, phylograms and ancestral sequences

Levels

ZOMBI2 is organized around four levels of evolution. A genome, a sequence or a trait always evolves along a species tree, so you run whichever you need, composed into one seeded, reproducible run.

One simulated dataset at all four levels: a species tree with its extinct lineages, the gene order of every surviving genome with homologues linked, the alignment behind one gene family, and two traits drifting together

  • Species trees — a birth–death process with rates that can shift in time, saturate with diversity or drift down the tree, plus mass extinctions, incomplete sampling and fossils.
  • Genomes — gene families under duplication, transfer, loss and origination, at three resolutions: gene families, ordered chromosomes with rearrangements, and nucleotide genomes, with real DNA along each chromosome.
  • Sequences — nucleotide (JC69, K80, HKY85, GTR) and protein substitution models run down each gene tree, with ancestral sequences at every node.
  • Traits — continuous traits that diffuse, revert to an optimum or shift at speciation, and discrete traits switching between states.

The four levels of evolution ZOMBI2 simulates: the species tree forks into genomes and traits, and sequences continue below genomes

Conditioning

Conditioning is a rate reading the state of a level that has already been grown. There are three parts: the driver, the level that is read; the modifier, which turns the driver's state into a factor; and the target, the rate it multiplies.

Conditioning: a habitat trait on the left, an arrow labelled drives running right to the gene loss rate and carrying a multiplier for each habitat state, and under the loss rate the expression you write on it, 0.25 times DrivenBy of habitat 

zombi2 species out/ --birth 1 --death 0.3 --n-extant 20 --seed 1
zombi2 traits  out/ --kind discrete --states aquatic,terrestrial --switch 0.4 --seed 1
zombi2 genomes out/ --loss "0.25 * DrivenBy('out/traits/trait_events.tsv', {'aquatic': 4.0})" --seed 1

Joining

Joining is what to reach for when neither level can be grown first, because each drives the other: one run grows both. A trait that speeds up speciation is the standard case: the tree shapes the trait's history and the trait shapes the tree, so the tree is an output of the joint run rather than an input to it.

Joining: body size drives the speciation rate, with the expression written on that rate shown beneath it, the rate creates the tree, and an arrow runs back from the tree to body size because the two grow at the same time 

zombi2 joint out/ --birth "1.0 * DrivenBy('trait', {'small': 1.0, 'large': 3.0})" \
    --states small,large --switch 0.3 --n-extant 100 --seed 1

Performance

A species tree of a million leaves takes a few seconds. On the same gene-family task, ZOMBI2 runs about 183× faster than the legacy ZOMBI v1 — both pure Python.

ZOMBI2 performance overview: (a) species-tree simulation scaling to millions of tips; (b) genome simulation at the family, ordered and nucleotide resolutions; (c) ZOMBI2 about 183 times faster than the legacy ZOMBI 1 on one shared 1,000-tip tree

Gallery

The gallery is a page of worked examples, one figure each, with the code that produced it: species trees, genomes, sequences, traits, conditioning and joining. Every figure is drawn with Phylustrator.

Citation

A dedicated ZOMBI2 paper is in preparation. Until then, cite the original ZOMBI.

License

ZOMBI2 is released under the MIT License.

Project links

Data verified by PyPI on Aug 2, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (0.44.0)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for AADavin from gravatar.com AADavin

Credits

Author: Adrián A. Davin

GitHub Statistics

Data verified by PyPI on Aug 2, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

MIT
View SPDX License List

Requires

Python >=3.10

Provides Extra

bench dev docs gallery reconparser

Tags

birth-death evolution gene families phylogenetics simulation

Classifiers

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

zombi2-0.25.0.tar.gz (6.8 MB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

zombi2-0.25.0-py3-none-any.whl (387.1 kB view details)

Uploaded Python 3

File details

Details for the file zombi2-0.25.0.tar.gz.

File metadata

  • Download URL: zombi2-0.25.0.tar.gz
  • Upload date:
  • Size: 6.8 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for zombi2-0.25.0.tar.gz
Algorithm Hash digest
SHA256 9badd95801fd359748826eb5b6b37a29b14358ef38a8e7fedd1f915e92a0ab52
MD5 4c1cfd92d6776cb0dd9b19c320c4026a
BLAKE2b-256 4854b604d00aa067841eb88650713a499698ca12774aa40804416fdd5a9f9f39

See more details on using hashes here.

Provenance

The following attestation bundles were made for zombi2-0.25.0.tar.gz:

Publisher: release.yml on AADavin/zombi2

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file zombi2-0.25.0-py3-none-any.whl.

File metadata

  • Download URL: zombi2-0.25.0-py3-none-any.whl
  • Upload date:
  • Size: 387.1 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for zombi2-0.25.0-py3-none-any.whl
Algorithm Hash digest
SHA256 84d8debd3477d1cd44bf9d859f2c1bf3482fed7bfb55f753537b93b98c4d8ad0
MD5 55d07347bd85ec46abe343d18171d407
BLAKE2b-256 bb0e51d6d53b202b7c5d4e25e7827298aa1edda72a208f518d0ac581e70842f1

See more details on using hashes here.

Provenance

The following attestation bundles were made for zombi2-0.25.0-py3-none-any.whl:

Publisher: release.yml on AADavin/zombi2

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Release history Release notifications | RSS feed

0.44.0

2 files

0.43.2

2 files

0.43.1

2 files

0.43.0

2 files

0.42.2

2 files

0.42.1

2 files

0.42.0

2 files

0.41.0

2 files

0.40.0

2 files

0.39.4

2 files

0.39.3

2 files

0.39.2

2 files

0.39.1

2 files

0.39.0

2 files

0.38.0

2 files

0.37.0

2 files

0.36.0

2 files

0.35.0

2 files

0.34.0

2 files

0.33.1

2 files

0.33.0

2 files

0.32.0

2 files

0.31.0

2 files

0.30.0

2 files

0.29.0

2 files

0.28.0

2 files

0.27.0

2 files

0.26.0

2 files

This release

0.25.0 This release

2 files

0.24.0

2 files

0.23.0

2 files

0.22.0

2 files

0.21.0

2 files

0.20.0

2 files

0.19.0

2 files

0.18.0

2 files

0.17.0

2 files

0.16.0

2 files

0.15.0

2 files

0.14.0

2 files

0.13.0

2 files

0.12.0

2 files

0.11.0

2 files

0.10.0

2 files

0.9.0

2 files

0.8.0

2 files

0.7.0

2 files

0.6.0

2 files

0.5.0

2 files

0.4.0

2 files

0.3.0

2 files

Yanked

0.2.0

2 files

Yanked reason: Outdated version, do not use

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page