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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.

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

  • 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.

Combining levels

Levels do not have to run side by side: one can drive another. Both ways of doing it are the same mechanism, DrivenBy(source, mapping), written on any rate. See conditioning and joining.

Conditioning

A rate reads 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 drives the gene loss rate on the right through a DrivenBy modifier, which carries a multiplier for each habitat state 

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

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 through a DrivenBy modifier, 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

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Credits

Author: Adrián A. Davin

GitHub Statistics

Data verified by PyPI on Jul 31, 2026
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Python >=3.10

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