## SynMut: Tools for Designing Synonymously Mutated Sequences with Different Genomic Signatures
*Haogao Gu, Leo L.M. Poon*
<img src="https://raw.githubusercontent.com/Koohoko/Koohoko.github.io/master/SynMut/images/sph_logo.png" alt="drawing" width="200" ALIGN="LEFT" />
##### This work was conducted in School of Public Health, The University of Hong Kong under the supervison of Prof. Leo Poon.
***
[DOI: 10.18129/B9.bioc.SynMut](https://doi.org/doi:10.18129/B9.bioc.SynMut)
<img border="0" src="https://bioconductor.org/shields/build/devel/bioc/SynMut.svg">
### Introduction
*SynMut* designs synonymous mutants for DNA sequences.
There are increasing demands on designing virus mutants with specific dinucleotide or codon composition. This tool can take both dinucleotide preference and/or codon usage bias into account while designing mutants. It also works well for desinging mutants with extremely over-/under- represented dinucleotides.
This tool was originally designed for generating recombinant virus sequences in influenza A virus to study the effects of different dinucleotide usage and codon usage, yet the functions provided in this package can be generic to a variety of other biological researches.
### Components of the package
### Installation
Use the below code to install the package.
```r
# Stable version
if (!requireNamespace("BiocManager"))
install.packages("BiocManager")
if (!requireNamespace("SynMut"))
BiocManager::install("SynMut")
# Development version
if (!requireNamespace("devtools"))
install.packages("devtools")
if (!requireNamespace("SynMut"))
devtools::install_github("Koohoko/SynMut")
```
### Example and methods
Details tutorial please refer to the [vignette](https://koohoko.github.io/SynMut/index.html).
The strategies and functionalities of the `codom_mimic` and `dinu_to` functions can be found at [here](https://koohoko.github.io/SynMut/algorithm.html).
### Find it at Bioconductor
https://bioconductor.org/packages/devel/bioc/html/SynMut.html
***
### Changelog
Changes in version 1.1.5 (2022-06-03)
+ Enhancement: add other non-standard genetic codes for functions codon_random, dinu_to, codon_mimic.
Changes in version 1.1.4 (2020-11-12)
+ bug fix: fix for function codon_mimic.
Changes in version 1.1.3 (2019-05-08)
+ Revise dinu_to.keep algorithm, enhance performance.
Changes in version 1.1.2 (2019-05-08)
+ Bug fix: "dinu_to" ifelse issue in get_optimal_codon.
Changes in version 1.1.1 (2019-05-06)
+ Bug fix: "dinu_to" fix wrong result with "keep == TRUE" parameter.
