doubletrouble

The major goal of doubletrouble is to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. Duplicates can be classified using four different classification schemes, which increase the complexity and level of details in a stepwise manner. The classification schemes and the duplication modes they can classify are:

Scheme	Duplication modes
binary	SD, SSD
standard	SD, TD, PD, DD
extended	SD, TD, PD, TRD, DD
full	SD, TD, PD, rTRD, dTRD, DD

Legend: SD, segmental duplication. SSD, small-scale duplication. TD, tandem duplication. PD, proximal duplication. TRD, transposon-derived duplication. rTRD, retrotransposon-derived duplication. dTRD, DNA transposon-derived duplication. DD, dispersed duplication.

Besides classifying gene pairs, users can also classify genes, so that each gene is assigned to a unique mode of duplication.

Users can also calculate substitution rates per substitution site (i.e., $K_a$, $K_s$ and their ratios $\frac{K_a}{K_s}$) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

Installation instructions

Get the latest stable R release from CRAN. Then install doubletrouble from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("doubletrouble")

And the development version from GitHub with:

BiocManager::install("almeidasilvaf/doubletrouble")

Citation

Below is the citation output from using citation('doubletrouble') in R. Please run this yourself to check for any updates on how to cite doubletrouble.

print(citation('doubletrouble'), bibtex = TRUE)
#> To cite doubletrouble in publications, use:
#> 
#>   Almeida-Silva F, Van de Peer Y doubletrouble: an R/Bioconductor
#>   package for the identification, classification, and analysis of gene
#>   and genome duplications. Bioinformatics, 41(2), btaf043. (2025).
#>   https://doi.org/10.1093/bioinformatics/btaf043
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications},
#>     author = {Fabricio Almeida-Silva and Yves {Van de Peer}},
#>     journal = {Bioinformatics},
#>     year = {2025},
#>     volume = {41},
#>     number = {2},
#>     pages = {btaf043},
#>     url = {https://academic.oup.com/bioinformatics/article/41/2/btaf043/7979242},
#>     doi = {10.1093/bioinformatics/btaf043},
#>   }

Please note that the doubletrouble was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the doubletrouble project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

• Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
• Code coverage assessment is possible thanks to codecov and covr.
• The documentation website is automatically updated thanks to pkgdown.
• The code is styled automatically thanks to styler.
• The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.