https://github.com/kullrich/msa2dist

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
https://github.com/kullrich/msa2dist

bioconductor-package bioinformatics dnds dnds-estimation iupac kaks msa2dist multiple-sequence-alignment r score-matrix

Last synced: 4 days ago
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MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

• Host: GitHub
• URL: https://github.com/kullrich/msa2dist
• Owner: kullrich
• License: gpl-3.0
• Created: 2021-12-22T19:42:12.000Z (almost 3 years ago)
• Default Branch: devel
• Last Pushed: 2024-11-02T08:52:22.000Z (5 days ago)
• Last Synced: 2024-11-02T09:25:46.599Z (5 days ago)
• Topics: bioconductor-package, bioinformatics, dnds, dnds-estimation, iupac, kaks, msa2dist, multiple-sequence-alignment, r, score-matrix
• Language: C++
• Homepage:
• Size: 602 KB
• Stars: 4
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

        
# MSA2dist 

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

## 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.