MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis.

Get the latest stable R release from CRAN. Then install MSA2dist from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("MSA2dist")

And the development version from GitHub with:

BiocManager::install("kullrich/MSA2dist")

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