MSA2dist

MSA2dist calculates pairwise distances for DNAStringSet/AAStringSet using custom scoring, conducts codon analyses (including dNdS), and estimates Dxy/FST

Bioconductor version: 3.24 · Package version: 1.17.8

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calculations which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances. DNAStringSet alignments can be analysed as codon alignments to look for synonymous and nonsynonymous substitutions (dN/dS) in a parallelised fashion using a variety of substitution models. Non-aligned coding sequences can be directly used to construct pairwise codon alignments (global/local) and calculate dN/dS without any external dependencies. In addition, MSA2dist provides population genetic analyses, including the calculation of nucleotide divergence between populations (Dxy) and genetic differentiation statistics (FST) from aligned sequence data.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MSA2dist")