CS-PSeq-Gen

CS-PSeq-Gen simulates protein sequence evolution along a reconstructed phylogeny to model sequence changes and analyze correlated amino-acid site evolution.

Key Features:

• Phylogeny-Constrained Simulations: Simulates protein sequence evolution constrained to a provided reconstructed phylogeny so substitutions follow known ancestral relationships.
• Control Over Evolutionary Parameters: Allows control over simulated tree structures and branch lengths, maintaining branch lengths around an average value.
• Investigation of Correlated Site Evolution: Generates simulation scenarios to detect correlations between amino acid positions and study co-evolutionary patterns.

Scientific Applications:

• Studying Protein Function: Infer interactions or dependencies between amino-acid positions by analyzing simulated co-evolution.
• Evolutionary Biology Research: Reconstruct and test hypotheses about protein evolutionary history using phylogeny-constrained simulations.
• Drug Design and Development: Assess correlated site evolution to inform targeting of specific protein sites in drug design.

Methodology:

Integrates phylogenetic data with sequence simulation algorithms to generate evolutionary scenarios that respect temporal and spatial constraints imposed by the phylogeny.