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: about 7 hours 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 (over 3 years ago)
- Default Branch: devel
- Last Pushed: 2025-03-28T08:08:24.000Z (3 months ago)
- Last Synced: 2025-03-28T09:24:36.534Z (3 months ago)
- Topics: bioconductor-package, bioinformatics, dnds, dnds-estimation, iupac, kaks, msa2dist, multiple-sequence-alignment, r, score-matrix
- Language: C++
- Homepage:
- Size: 615 KB
- Stars: 4
- Watchers: 1
- 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. 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.