CastNet

CastNet simulates genome evolution by integrating sequence and regulatory coevolution within a multi-genic framework.

Key Features:

• Coevolutionary Framework: Models genomes as collections of interdependent genes whose evolutionary trajectories are interconnected through coevolution.
• Regulatory Interactions and Phenotypes: Simulates regulatory interactions among genes to produce gene expression profiles that determine fitness.
• Genetic Algorithm for Evolution: Evolves populations of genomes using a genetic algorithm across user-defined phylogenies.
• Link Between Sequence and Regulatory Evolution: Models regulatory mutations as responses to sequence mutations, linking rates of sequence evolution with changes in regulatory parameters.
• Coevolutionary Signal Detection: Detects coevolutionary signals among genes active in Gene Regulatory Networks (GRNs) and neutral evolution in genes outside these networks.

Scientific Applications:

• Comparative Genomics: Simulates coevolution of sequences and regulatory interactions to inform evolutionary relationships and functional adaptations across species.
• Study of Coevolutionary Dynamics: Provides a framework to investigate how genes coevolve within regulatory networks and how regulatory interactions shape evolutionary trajectories.
• Molecular Evolution Research: Enables study of molecular evolution where sequence coevolution and regulatory change contribute to adaptive and neutral processes.

Methodology:

Uses a genetic algorithm to evolve genome populations along user-defined phylogenies, simulates regulatory interactions to generate gene expression phenotypes and fitness, models regulatory mutations in response to sequence mutations, and assesses coevolutionary signals among genes and within Gene Regulatory Networks (GRNs).