NetTest

NetTest characterizes directed or rooted reticulate phylogenetic networks to assess structural classes and the implications of evolutionary events such as recombination, hybridization, and gene transfer in DNA and protein sequence evolution.

Key Features:

• Categorization Capabilities: Assigns phylogenetic networks to theoretical classes including "Tree," "Tree-sibling," "Tree-child," "Galled-tree," and "Time-consistent."
• Complexity Analysis: Evaluates network complexity with attention to factors such as population recombination rates.
• Statistical Parsimony Support: Processes statistical parsimony phylogenetic networks, including those estimated by programs like TCS.
• Dataset Application: Has been applied to approximately 5,000 DNA alignments sourced from NCBI PopSet and Polymorphix.
• Correlation Analysis: Examines relationships between network characterization and nucleotide diversity.

Scientific Applications:

• Reticulate evolution characterization: Classifies networks that represent recombination, hybridization, and gene transfer events in DNA and protein sequences.
• Empirical network analysis: Analyzes large collections of statistical parsimony networks derived from NCBI PopSet and Polymorphix alignments.
• Genetic diversity studies: Correlates network structure and complexity with nucleotide diversity to investigate evolutionary dynamics.

Methodology:

Processes statistical parsimony phylogenetic networks derived from DNA alignments, assesses their compatibility with established network classes (Tree, Tree-sibling, Tree-child, Galled-tree, Time-consistent), and examines correlations between network complexity and nucleotide diversity.