SimPlot++

SimPlot++ generates sequence similarity plots and detects homologous recombination events to support evolutionary and comparative analyses of nucleotide and amino acid sequences.

Key Features:

• Sequence Similarity Plots: Generates publication-quality plots using 63 nucleotide and 20 amino acid distance models.
• Recombination Detection: Detects intergenic and intragenic recombination using statistical tests including Φ (Phi), Max-χ² (Chi-squared), NSS (Nearest Sequenced Segment), and proportion tests.
• Interactive Sequence Similarity Networks: Creates and analyzes interactive sequence similarity networks for exploring complex genetic relationships.
• Multicore Data Processing: Employs multicore parallel processing to accelerate analyses on large datasets.
• Distance Calculability Diagnostics: Provides diagnostics to assess distance calculability and the reliability of similarity measures.

Scientific Applications:

• Evolutionary Biology: Investigating genetic variation and evolutionary relationships using nucleotide and amino acid sequence analyses.
• Phylogenetic Studies: Assessing sequence similarity and recombination to inform phylogenetic inference.
• Viral Evolution: Analyzing recombination and sequence similarity among viral strains.
• Comparative Genomics: Comparing nucleotide and amino acid sequences across species or strains to study divergence and conservation.

Methodology:

Models sequence distances with 63 nucleotide and 20 amino acid distance models, applies multiple statistical tests (Φ, Max-χ², NSS, proportion tests) to detect intergenic and intragenic recombination, includes diagnostics for distance calculability, and performs analyses using multicore parallel processing.