ASaturA

ASaturA assesses mutational saturation in amino acid sequences to distinguish frequent and rare substitutions and to refine pairwise evolutionary distances for phylogenetic inference.

Key Features:

• Visualization of Mutational Saturation: Generates plots of observed frequent and rare amino acid replacements versus evolutionary distance between sequence pairs.
• Substitution Probability Matrices: Uses PAM and BLOSUM substitution probability matrices to classify high- and low-probability amino acid substitutions.
• Saturation-aware Distance Calculation: Identifies saturated sites and recalculates evolutionary distances by excluding those sites to reduce saturation artifacts.
• Pairwise Distance-based Phylogenetic Inference: Infers evolutionary trees using pairwise distance methods computed after excluding saturated sites, allowing detection of alternative topologies such as fish gene duplicates appearing as sister sequences.
• Frequency Classification of Replacements: Distinguishes frequent versus rare amino acid replacements for downstream analyses.

Scientific Applications:

• Phylogenetic reconstruction: Improves accuracy of evolutionary tree reconstruction by accounting for mutational saturation in amino acid data.
• Ancient gene duplication analysis: Tests hypotheses about the timing and nature of gene duplication events, including evaluations of whether fish duplicates predate divergence from tetrapods.
• Comparative genomics of Actinopterygii and Sarcopterygii: Supports analyses addressing origins of gene duplications and hypotheses of genome duplication or differential gene loss in ray-finned fishes and their tetrapod relatives.

Methodology:

Input amino acid sequences; analyze saturation using substitution probability matrices (PAM, BLOSUM) to classify frequent and rare substitutions and identify saturated sites; generate plots of substitution frequency versus evolutionary distance; recalculate evolutionary distances excluding saturated sites; construct evolutionary trees using pairwise distance methods.