# Chaos Game Representation for Phylogenetic Analysis

## Documentation for package ‘CGRphylo2’ version 0.99.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

calculateDistanceMatrix | Calculate pairwise distance matrix for multiple sequences
cgrplot | Generate CGR plot coordinates for a DNA sequence
create_meta | Create metadata table for sequences
filter_N | Filter sequences by N content
from_DNAStringSet | Convert a DNAStringSet to a named list of sequences
matrixDistance | Calculate distance between two CGR frequency matrices
parallelCGR | Parallel computation of CGR frequency matrices
plot_cgr | Plot CGR with customization options
saveMegaDistance | Save distance matrix in MEGA format
savePhylipDistance | Save distance matrix in PHYLIP format