Zombi

Zombi simulates the evolution of species, genomes, and sequences in silico, incorporating extinct lineages to generate phylogenetic trees that account for both extant and extinct taxa.

Key Features:

• Extinct lineage simulation: Simulates genome evolution in extinct lineages to include extinct taxa in evolutionary scenarios.
• Species tree generation: Generates species trees with adjustable speciation and extinction rates to model varying macroevolutionary dynamics.
• Gene tree–species tree reconciliation: Outputs reconciliations between gene trees and species trees to track gene family evolution and lineage-specific events.
• Intergenic sequence simulation: Simulates intergenic sequences with variable lengths to produce realistic genomic sequence data.

Scientific Applications:

• Evolutionary hypothesis testing: Enables testing of evolutionary hypotheses under controlled simulated conditions.
• Speciation and extinction dynamics: Provides insights into speciation and extinction processes by explicitly modeling extinct lineages and rate variation.
• Phylogenetics, molecular evolution, and comparative genomics: Produces species trees, gene trees, and simulated sequences for analyses in phylogenetics, molecular evolution, and comparative genomics.

Methodology:

Simulates species trees with adjustable speciation and extinction rates; simulates genome evolution including extinct lineages; simulates intergenic sequences of variable lengths; and outputs reconciled gene trees and species trees.