parazitCUB

parazitCUB analyzes codon usage bias (CUB) in parasites to assess parasite–host codon co-adaptation.

Key Features:

• Scalability and Efficiency: Handles large datasets and supports analysis of multiple parasite genomes.
• Indices Calculation: Computes several codon usage bias indices for quantification of CUB.
• Cluster Analysis: Groups similar codon usage patterns to identify evolutionary relationships and adaptations.
• Multivariate Analysis: Applies multivariate statistical methods to explore factors influencing codon usage.
• Data Visualization: Produces visualizations to interpret codon usage and comparative analyses.

Scientific Applications:

• Parasite–host co-adaptation analysis: Assesses molecular-level codon usage relationships between parasites and their hosts.
• Prediction of parasite characteristics: Infers traits of novel parasites based on codon usage patterns.
• Study of evolutionary pressures: Investigates selective and mutational forces shaping parasite genomes using CUB metrics.

Methodology:

Implemented as an R package; computational methods include calculation of codon usage indices, cluster analysis, multivariate statistical analyses, and data visualization.