Zombi

Zombi is a software tool that simulates the evolution of species, genomes, and sequences in silico. It stands out from existing simulators by incorporating several unique features:

1. Zombi is the first tool to consider the evolution of genomes in extinct lineages, providing a more comprehensive evolutionary perspective.

2. It can generate species trees with pre-defined variations in speciation and extinction rates over time, allowing for more realistic evolutionary scenarios.

3. The tool explicitly simulates intergenic sequences of variable length, offering a more detailed representation of genomes.

4. Zombi outputs gene tree-species tree reconciliations, enabling users to study the relationship between genes and species evolution.

Topic

Phylogeny

Detail

  • Operation: Phylogenetic tree comparison;Phylogenetic tree reconstruction;Phylogenetic species tree construction

  • Software interface: Command-line user interface

  • Language: Python

  • License: Not stated

  • Cost: Free of charge

  • Version name: https://github.com/AADavin/ZOMBI/

  • Credit: The European Research Council under the European Union’s Horizon 2020 research and innovation programme.

  • Input: -

  • Output: -

  • Contact: Adrián A Davín aaredav@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages.
  • Davín AA, et al. Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages. Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages. 2020; 36:1286-1288. doi: 10.1093/bioinformatics/btz710
  • https://doi.org/10.1093/BIOINFORMATICS/BTZ710
  • PMID: 31566657
  • PMC: PMC7031779

Download and documentation

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