Genonets

Genonets constructs and analyzes genotype networks to represent relationships among genotypes that share phenotypes and to study robustness, evolvability, and the organization of genotype spaces.

Key Features:

• Construction of genotype networks: Builds genotype networks from DNA, RNA, amino acid, or binary sequences and supports categorical and univariate phenotypes.
• Mutation adjacency definition: Represents vertices as genotypes with identical phenotypes and connects vertices with edges when genotypes differ by a single small mutation.
• Topology and topography analysis: Analyzes network topology and topography to assess relationships between robustness and evolvability and to characterize navigability of genotype spaces.
• Visualization of networks: Provides visualization options to explore and represent complex genotype network structures.

Scientific Applications:

• RNA macromolecules: Analyze genotype-phenotype maps and evolutionary properties of RNA sequences.
• Transcriptional regulatory circuits: Study genotype networks underlying regulatory circuit function and variation.
• Evolutionary biology: Investigate robustness, evolvability, and the organization and navigability of genotype spaces under mutation and selection.

Methodology:

Automates construction, analysis, and visualization of genotype networks by applying graph theory: vertices represent genotypes with identical phenotypes and edges connect genotypes that differ by a single small mutation.