PoSeiDon

PoSeiDon performs recombination detection, substitution model estimation, phylogeny construction, and identification of positively selected sites on homologous protein-coding sequences to analyze molecular evolution.

Key Features:

• Alignment Construction: Constructs optimal alignments from homologous protein-coding sequences for downstream evolutionary analyses.
• Substitution Model Estimation: Estimates the best-fitting substitution model for the input data to inform evolutionary inference.
• Recombination Analysis: Detects potential recombination events and identifies recombination fragments within alignments.
• Phylogeny Construction: Builds phylogenetic trees for the full alignment and for identified recombination fragments.
• Detection of Positively Selected Sites: Identifies sites under significant positive selection using multiple models applied to full alignments and recombination segments.

Scientific Applications:

• Molecular Evolution Studies: Analyzes adaptive changes and mutation hotspots in protein-coding genes to study evolutionary pressures.
• Viral Evolution and Virus–Host Interactions: Investigates rapid viral evolution and virus–host interactions by detecting recombination and positively selected sites.
• Phylogenetic Assessment: Assesses the impact of recombination on phylogenetic inference and genetic diversity.

Methodology:

PoSeiDon uses Nextflow for workflow management, Docker for containerization, and integrates outputs from various bioinformatics tools.