Patristic

Patristic computes patristic distances from phylogenetic trees to quantify genetic change represented by branch lengths.

Key Features:

• Versatile Input Handling: Accepts phylogenetic tree files in various tree file formats for analysis.
• Patristic Distance Calculation: Computes patristic distances that quantify genetic changes along tree branches.
• Integration with Other Measures: Correlates patristic distances with other genetic distance measures for comparative analyses.
• Graphical and Statistical Interpretation: Produces graphical representations and performs statistical analyses on distance matrices.
• Data Management Features: Accepts associated metadata such as isolation dates and supports reordering of matrices by matching species or gene labels.
• Statistical Analysis Tools: Includes functions to calculate commonly used statistical measures for evaluating mutation rates and substitutional saturation.

Scientific Applications:

• Mutation Rates: Enables investigation of genomic mutation rates by analyzing patristic distance accumulation.
• Substitutional Saturation: Assesses substitutional saturation to evaluate evolutionary signal over time.
• Viral Evolution: Supports analyses of viral evolutionary dynamics where rapid mutation and large datasets are common.

Methodology:

Derives patristic distances from phylogenetic trees and integrates those distances with other genetic measures for statistical and graphical analysis.