CGRphylo2
This is the development version of CGRphylo2; to use it, please install the devel version of Bioconductor.
Chaos Game Representation for Phylogenetic Analysis
Bioconductor version: Development (3.24)
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)
Author: Amarinder Singh Thind [aut, cre]
Maintainer: Amarinder Singh Thind <thind.amarinder at gmail.com>
citation("CGRphylo2")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("CGRphylo2")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CGRphylo2")| Introduction to CGRphylo2 | HTML | R Script |
| Reference Manual |
Details
| biocViews | Alignment, Classification, Clustering, Genetics, MultipleComparison, MultipleSequenceAlignment, Phylogenetics, SequenceMatching, Software, Visualization |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | BiocParallel, Biostrings |
| System Requirements | |
| URL | https://github.com/amarinderthind/CGRphylo2 |
| Bug Reports | https://github.com/amarinderthind/CGRphylo2/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), ape, seqinr, stringr, ggplot2, RColorBrewer, treeio |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CGRphylo2_0.99.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | CGRphylo2_0.99.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CGRphylo2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CGRphylo2 |
| Bioc Package Browser | https://code.bioconductor.org/browse/CGRphylo2/ |
| Package Short Url | https://bioconductor.org/packages/CGRphylo2/ |
| Package Downloads Report | Download Stats |