SELVa

SELVa simulates sequence evolution under dynamically changing fitness landscapes to model substitutions across phylogenies influenced by environmental shifts and epistatic interactions.

Key Features:

• Dynamic fitness landscapes: Represents a fitness landscape as a vector of fitness values for different variants at a specific site and allows those landscapes to change over time due to environmental changes or substitutions at epistatically interacting sites.
• Substitution modeling on phylogenies: Simulates the substitution process within evolving lineages that form phylogenies of arbitrary shapes.
• Customizable landscape-change rules: Enables definition and implementation of various rules governing when and how fitness landscapes change.
• Per-site modeling: Models fitness and evolutionary dynamics at the level of individual sites.
• Implementation: Implemented in Java.

Scientific Applications:

• Molecular evolution: Simulates sequence-level evolutionary dynamics to study how shifting fitness landscapes affect molecular substitutions.
• Phylogenetics: Evaluates how landscape variation across sites and lineages influences inferred evolutionary trajectories on arbitrary phylogenies.
• Epistasis and landscape dynamics: Investigates effects of substitutions at interacting sites on local fitness landscapes and subsequent evolution.
• Adaptive response to environmental change: Models how environmental shifts that alter fitness landscapes drive adaptive or nonadaptive sequence changes.

Methodology:

Simulates sequence evolution by representing per-site fitness landscapes as vectors of fitness values, modeling substitutions on phylogenies of arbitrary shape, and applying user-defined rules to change landscapes over time.