Package: CGRphylo2
Type: Package
Title: Chaos Game Representation for Phylogenetic Analysis
Version: 0.99.2
Date: 2026-06-12
Authors@R: person("Amarinder Singh", "Thind", 
                  email = "thind.amarinder@gmail.com",
                  role = c("aut", "cre"),
                  comment = c(ORCID = "0000-0003-4592-0380"))
Description: 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>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: BiocParallel, Biostrings
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), ape,
        seqinr, stringr, ggplot2, RColorBrewer, treeio
VignetteBuilder: knitr
biocViews: Phylogenetics, Genetics, SequenceMatching, Alignment,
        Clustering, Visualization, Software, MultipleSequenceAlignment,
        MultipleComparison, Classification
BugReports: https://github.com/amarinderthind/CGRphylo2/issues
URL: https://github.com/amarinderthind/CGRphylo2
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
git_url: https://git.bioconductor.org/packages/CGRphylo2
git_branch: devel
git_last_commit: 05a7d66
git_last_commit_date: 2026-06-11
Repository: Bioconductor 3.24
Date/Publication: 2026-06-26
NeedsCompilation: no
Packaged: 2026-06-26 19:58:16 UTC; biocbuild
Author: Amarinder Singh Thind [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4592-0380>)
Maintainer: Amarinder Singh Thind <thind.amarinder@gmail.com>
Built: R 4.6.0; ; 2026-06-27 03:33:38 UTC; unix
