# ------------------------------------------------ # CITATION.cff file created with {cffr} R package # See also: https://docs.ropensci.org/cffr/ # ------------------------------------------------ cff-version: 1.2.0 message: 'To cite package "CGRphylo2" in publications use:' type: software license: GPL-3.0-only title: 'CGRphylo2: Chaos Game Representation for Phylogenetic Analysis' version: 0.99.2 abstract: 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) . authors: - family-names: Thind given-names: Amarinder Singh email: thind.amarinder@gmail.com orcid: https://orcid.org/0000-0003-4592-0380 repository: https://bioc.r-universe.dev repository-code: https://github.com/amarinderthind/CGRphylo2 commit: 05a7d6639feaee62e07672f06b7c9758c637318c url: https://github.com/amarinderthind/CGRphylo2 date-released: '2026-06-12' contact: - family-names: Thind given-names: Amarinder Singh email: thind.amarinder@gmail.com orcid: https://orcid.org/0000-0003-4592-0380