CASS

CASS simulates and samples protein sequences using an explicit genotype-to-phenotype mapping that integrates protein structural and functional constraints to model protein sequence evolution.

Key Features:

• Genotype-to-Phenotype Mapping: Explicitly models the relationship between genetic sequence and resulting phenotypic traits, incorporating structural and functional aspects of proteins.
• Structure-Specific Properties: Reproduces structure-specific properties observed in protein sequence evolution, including spatial and temporal variation in evolutionary rates.
• Thermodynamic Influence: Enables exploration of hypotheses regarding the impact of thermodynamics on molecular evolution.

Scientific Applications:

• Protein Evolution: Investigating mechanisms and patterns of protein sequence evolution.
• Structure–Function Relationships: Analyzing how protein structural features affect function and evolutionary constraints.
• Thermodynamic Hypotheses: Testing hypotheses about thermodynamic contributions to molecular evolution.
• Evolutionary Scenario Simulation: Generating realistic evolutionary scenarios for theoretical studies and bioinformatics analyses.

Methodology:

Implemented in object-oriented C++.