saveMegaDistance.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/distances_and_export.R
\name{saveMegaDistance}
\alias{saveMegaDistance}
\title{Save distance matrix in MEGA format}
\usage{
saveMegaDistance(filename, distance_matrix)
}
\arguments{
\item{filename}{Character. Output filename (typically with .meg extension).}

\item{distance_matrix}{Numeric matrix. A square distance matrix with row and
column names corresponding to sequence identifiers.}
}
\value{
NULL. Writes file as a side effect.
}
\description{
Exports a distance matrix to MEGA format for use with MEGA software for
phylogenetic tree visualization and analysis.
}
\details{
MEGA (Molecular Evolutionary Genetics Analysis) is widely used for
phylogenetic analysis. This function creates a distance matrix file
compatible with MEGA's format specifications.
}
\examples{
# Build a small symmetric distance matrix
dist_mat <- matrix(
    c(0.00, 0.12, 0.25,
      0.12, 0.00, 0.18,
      0.25, 0.18, 0.00),
    nrow = 3
)
rownames(dist_mat) <- colnames(dist_mat) <- c("Seq1", "Seq2", "Seq3")

# Save to a temporary file (no permanent files written during checks)
out <- tempfile(fileext = ".meg")
saveMegaDistance(out, dist_mat)

# Inspect the first few lines of the output
writeLines(readLines(out, n = 8))

}