# ZOMBI2

> ZOMBI2 simulates the evolution of species trees, genomes, sequences and traits, each on its own,
> conditioned on another, or jointly, and records the true history behind every dataset. Pure
> Python, `pip install zombi2`, MIT.

An agent that will use ZOMBI2 in a project starts here, one file that installs it and says how it is
driven: https://aadavin.github.io/zombi2/docs/agent-setup/prompt.txt

## Manual

- [Introduction](https://aadavin.github.io/zombi2/docs/guide/introduction/)
- [Species trees](https://aadavin.github.io/zombi2/docs/guide/species-trees/)
- [Genomes I: gene families](https://aadavin.github.io/zombi2/docs/guide/genomes/)
- [Genomes II: ordered](https://aadavin.github.io/zombi2/docs/guide/genomes-ordered/)
- [Genomes III: nucleotide](https://aadavin.github.io/zombi2/docs/guide/genomes-nucleotide/)
- [Sequences](https://aadavin.github.io/zombi2/docs/guide/sequences/)
- [Traits](https://aadavin.github.io/zombi2/docs/guide/traits/)
- [Dependent runs](https://aadavin.github.io/zombi2/docs/guide/conditioning/)
- [The rate grammar](https://aadavin.github.io/zombi2/docs/rates/)
- [Output files](https://aadavin.github.io/zombi2/docs/output-files/)
- [Tools that read a run](https://aadavin.github.io/zombi2/docs/tools/)

## Reference

- [Python API](https://aadavin.github.io/zombi2/docs/api/)
- [Gallery, every figure with its code](https://aadavin.github.io/zombi2/gallery.html)
- [Repository](https://github.com/AADavin/zombi2)
- [Cite: Zenodo DOI 10.5281/zenodo.23168059](https://doi.org/10.5281/zenodo.23168059)