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
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-11 23:22:15 UTC
RemoteUrl: https://github.com/bioc/CGRphylo2
RemoteRef: HEAD
RemoteSha: 05a7d6639feaee62e07672f06b7c9758c637318c
NeedsCompilation: no
Packaged: 2026-06-28 11:13:11 UTC; root
Author: Amarinder Singh Thind [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4592-0380>)
Maintainer: Amarinder Singh Thind <thind.amarinder@gmail.com>
Built: R 4.6.1; ; 2026-06-28 11:14:45 UTC; windows
