TreeSAAP

TreeSAAP analyzes selective influences on 31 structural and biochemical amino acid properties during cladogenesis to detect and quantify adaptive changes in protein evolution.

Key Features:

• Comprehensive property analysis: Evaluates 31 distinct structural and biochemical amino acid properties to characterize physicochemical shifts associated with substitutions.
• Phylogenetic mapping: Analyzes phylogenetic trees and maps inferred amino acid changes onto branches to localize evolutionary changes across clades.
• Goodness-of-fit tests: Performs goodness-of-fit tests to compare observed property changes against neutral expectations.
• Categorical statistical tests: Conducts categorical statistical tests to assess the significance of selective influences and distinguish selection from drift.

Scientific Applications:

• Protein evolution and adaptation: Quantifies selective pressures on amino acids to identify adaptive substitutions affecting protein structure and function during cladogenesis.
• Testing selection hypotheses: Provides statistical evidence to test hypotheses of natural selection versus neutral evolution in molecular datasets.

Methodology:

Analyzes phylogenetic trees to trace amino acid changes across clades, maps those changes onto tree branches, evaluates 31 amino acid properties, and applies goodness-of-fit and categorical statistical tests.