CoreSimul

CoreSimul simulates prokaryotic genome evolution with explicit modeling of homologous recombination.

Key Features:

• Forward-Time Simulation: Operates as a forward-in-time simulator tailored to prokaryotic populations, in contrast to coalescent-based approaches that often assume neutral evolution.
• Homologous Recombination Modeling: Explicitly models homologous recombination processes that differ from meiotic recombination in sexual organisms.
• Phylogenetic Tree-Guided Simulations: Uses phylogenetic trees to guide simulations and incorporate evolutionary relationships and historical context.
• Substitution Models (including codon selection): Implements various nucleotide and codon-aware substitution models, including models that account for codon selection.
• Flexibility and Adaptability: Supports simulation scenarios under strong selective pressures to model diverse prokaryotic evolutionary dynamics.

Scientific Applications:

• Recombination Impact Studies: Analyze the effects of homologous recombination on genomic variation and lineage relationships in prokaryotes.
• Core Genome Evolution: Simulate evolution of core genomes within phylogenetic frameworks to study divergence and conservation patterns.
• Model Evaluation and Selection Studies: Compare the effects of different substitution models, including codon-selection models, on inferred evolutionary outcomes and adaptive mechanisms.

Methodology:

Forward-time population simulation with explicit homologous recombination, phylogenetic tree-guided sequence evolution, and implementation of multiple substitution models including codon-selection-aware models.