# MSA2dist <a href="https://www.bioconductor.org/packages/release/bioc/html/MSA2dist.html"><img src="man/figures/logo.png" align="right" height="160" /></a> `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. ## Installation instructions Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `MSA2dist` from [Bioconductor](http://bioconductor.org/) using the following code: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("MSA2dist") ``` And the development version from [GitHub](https://github.com/kullrich/MSA2dist) with: ``` r BiocManager::install("kullrich/MSA2dist") ``` ## Code of Conduct - Participation guidelines This repository adhere to [Contributor Covenant](http://contributor-covenant.org) code of conduct for in any interactions you have within this project. (see [Code of Conduct](https://github.com/kullrich/MSA2dist/blob/master/CODE_OF_CONDUCT.md)) See also the policy against sexualized discrimination, harassment and violence for the Max Planck Society [Code-of-Conduct](https://www.mpg.de/11961177/code-of-conduct-en.pdf). By contributing to this project, you agree to abide by its terms.