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Identification and classification of duplicated genes

Bioconductor version: Release (3.19)

doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

Author: Fabrício Almeida-Silva [aut, cre] , Yves Van de Peer [aut]

Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at>

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biocViews Classification, ComparativeGenomics, FunctionalGenomics, Network, Phylogenetics, Software, WholeGenome
Version 1.4.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2.0)
Imports syntenet, GenomicRanges, Biostrings, mclust, MSA2dist(>= 1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi, GenomicFeatures, BiocParallel
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Suggests txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork, BiocStyle, rmarkdown, covr, sessioninfo
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Source Package doubletrouble_1.4.0.tar.gz
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