ArticleBioinformatics (Oxford, England)2020
Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Augmenting microbial phylogenomic signal with tailored marker gene sets.Nature communications · 2025Article
- The path-label reconciliation (PLR) dissimilarity measure for gene trees.Algorithms for molecular biology : AMB · 2025Article
- Reconstructing rearrangement phylogenies of natural genomes.Algorithms for molecular biology : AMB · 2025Article
- SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.Nucleic acids research · 2025Article
- Unifying duplication episode clustering and gene-species mapping inference.Algorithms for molecular biology : AMB · 2024Article
- Multiple independent losses of sporulation and peptidoglycan in theMicrobial genomics · 2024Article
- OrthoPhy: A Program to Construct Ortholog Data Sets Using Taxonomic Information.Genome biology and evolution · 2023Article
- Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates.Bioinformatics (Oxford, England) · 2023Article
- GPTree Cluster: phylogenetic tree cluster generator in the context of supertree inference.Bioinformatics advances · 2023Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- Ghost lineages can invalidate or even reverse findings regarding gene flow.PLoS biology · 2022Article
- Simulating domain architecture evolution.Bioinformatics (Oxford, England) · 2022Article
- Benchmarking the topological accuracy of bacterial phylogenomic workflows usingMicrobial genomics · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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Abstract
summaryHere we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have not to date been combined in a single simulator, such as the possibility of generating species trees with a pre-defined variation of speciation and extinction rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree-species tree reconciliations. AVAILABILITY AND IMPLEMENTATION: Source code and manual are freely available in https://github.com/AADavin/ZOMBI/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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