CoPAP

CoPAP infers co-evolving characters (genes, restriction sites, introns, indels, methylation sites) from phyletic presence–absence patterns by modeling co-occurring gains and losses along phylogenetic trees to detect coevolutionary relationships.

Key Features:

• Probabilistic methodologies: Uses probabilistic models to infer coevolutionary relationships from presence–absence data and ancestral gain and loss events.
• Network analysis and visualization: Provides network-based analysis and visualization to represent interactions among co-evolving entities.
• Algorithm comparison platform: Compares different coevolution detection algorithms using simulated data containing pairs of coevolving sites and independent sites.
• Performance evaluation on simulations: Demonstrated superior performance relative to alternative methods for detecting co-evolutionary patterns using simulated datasets.

Scientific Applications:

• Evolutionary biology and genomics: Identification of clusters of coevolving genes that correspond to biosynthesis pathways and cellular modules across genomes.
• Bacterial gene coevolution analysis: Analysis of coevolution among thousands of bacterial genes, exemplified by a study across 681 genomes to detect biologically meaningful clusters.

Methodology:

Analysis of presence–absence data from multiple genomes to infer ancestral gain and loss events using probabilistic models that detect co-occurring gains and losses in phyletic patterns along phylogenetic trees.