CGRphylo2

Chaos Game Representation for Phylogenetic Analysis

Bioconductor version: 3.24 · Package version: 0.99.2

An alignment-free phylogenetic analysis method for viral genomes using Chaos Game Representation (CGR), a technique based on statistical physics concepts. Viruses exhibit high mutation rates, facilitating rapid evolution and emergence of new species, subspecies, strains, and recombinant forms. Accurate classification is crucial for understanding viral evolution and therapeutic development. Traditional phylogenetic methods require sequence alignment, which is computationally intensive. CGRphylo2 addresses this by implementing CGR-based whole-genome comparison that is fast, accurate, and computationally efficient. The package successfully classifies closely related viral lineages (demonstrated on SARS-CoV-2 lineages A and B), identifies recombinants (such as the XBB variant), and distinguishes multiple strains simultaneously. It processes sequences 5-13.7x faster than alignment-based methods (Clustal-Omega) with linear computational scaling. As a k-mer based approach, it enables simultaneous comparison of numerous closely-related sequences of different lengths. The package creates frequency matrices for distance calculations and phylogenetic tree construction, with outputs compatible with standard formats (MEGA, PHYLIP, Newick). Methods are based on Thind and Sinha (2023) <doi:10.2174/0113892029264990231013112156>.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CGRphylo2")