ZOMBI2 0.3.0

The first release of the rewritten ZOMBI2 — a phylogenetic simulator of species trees, genomes, molecular sequences, and traits, as a pure-Python library and command-line interface. It simulates each level independently, conditioned, or jointly, and records the true history behind every dataset.

pip install zombi2

What it does

• Species trees — birth–death with time / diversity / inherited-rate modifiers, mass extinctions, incomplete sampling, and fossils.
• Genomes, three resolutions:
  • unordered — gene families under duplication, transfer, loss, and origination;
  • ordered — chromosomes with inversions, transpositions, and translocations;
  • nucleotide — genes and intergenes over a base-pair coordinate space.
    Each resolution recovers the true gene trees.
• Sequences — nucleotide and protein substitution models along the gene trees, with strict and relaxed molecular clocks; emits alignments, ancestral sequences, and phylograms (branch lengths in substitutions/site).
• Traits — continuous (Brownian) and discrete trait evolution along the species tree.
• Conditioning and joining — grow one level driven by another.
• Tools — exact ortholog / paralog / xenolog homology tables and read-back utilities.

Notes

• Pure Python (numpy + tqdm); no build step, no compiled extension.
• Supersedes 0.2.0, which is yanked. 0.3.0 is the clean core.

Links

• Documentation: https://aadavin.github.io/zombi2/docs/
• Manual (PDF): https://aadavin.github.io/zombi2/zombi2-manual.pdf