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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

Each level is its own subcommand. Here a dated species tree, then gene families evolving along it under duplication, transfer, loss and origination, then sequences down each gene tree, then a trait evolving along the tree:

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 --origination 0.5 --seed 42
zombi2 sequences out/ --model hky85 --length 1000 --divergence 0.2 --seed 1
zombi2 traits    out/ --kind continuous --rate 1.0 --seed 1

Each command says where it wrote and refreshes out/run.zombi2 — a one-page, plain-text report of the whole run: every file it wrote and what each holds, the parameters, and the exact commands to reproduce it. Open that first. zombi2 <command> -h documents each of species, genomes, sequences and traits, with its own examples.

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

from zombi2 import species, genomes

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, seed=42)

g.gene_trees                    # the true gene tree of every family
g.write("run/")                 # the event log and the copy-number profiles

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. Extinct lineages are kept, so the complete tree and the extant one are both available.
  • Genomes — gene families under duplication, transfer, loss and origination, at three resolutions: gene families, ordered chromosomes with rearrangements, and nucleotide genomes where genes are blocks of DNA.
  • 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

A level can be conditioned on another — a rate reads a value some other level produced — or the two can be grown jointly, when neither can be simulated first because each drives the other. Both are one mechanism, DrivenBy(source, mapping), on any rate. See conditioning and joining.

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

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Python >=3.10

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