title: CDROM: Classification of Duplicate gene RetentiOn Mechanisms.
abstract: BACKGROUND
  Gene duplication is a major source of new genes that is thought to play an important role in phenotypic innovation. Though several mechanisms have been hypothesized to drive the functional evolution and long-term retention of duplicate genes, there are currently no software tools for assessing their genome-wide contributions. Thus, the evolutionary mechanisms by which duplicate genes acquire novel functions remain unclear in a number of taxa.
  
  
  RESULTS
  In a recent study, researchers developed a phylogenetic approach that uses gene expression data from two species to classify the mechanisms underlying the retention of duplicate genes (Proc Natl Acad Sci USA 110:1740917414, 2013). We have implemented their classification method, as well as a more generalized method, in the R package CDROM, enabling users to apply these methods to their data and gain insights into the origin of novel biological functions after gene duplication. The CDROM R package, source code, and user manual for the R package are available for download from CRAN at https://cran.rstudio.com/web/packages/CDROM/ . Additionally, the CDROM R source code, user manual for running CDROM from the source code, and sample dataset used in this manuscript can be accessed at www.personal.psu.edu/rua15/software.html .
  
  
  CONCLUSIONS
  CDROM is the first software package that enables genome-wide classification of the mechanisms driving the long-term retention of duplicate genes. It is user-friendly and flexible, providing researchers with a tool for studying the functional evolution of duplicate genes in a variety of taxa.
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
authors.forename: Brent R
authors.initials: BR
authors.lastname: Perry
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. rassis@psu.edu.
authors.forename: Raquel
authors.initials: R
authors.lastname: Assis
mesh_terms: D000818:Animals; D016251:CD-ROM; D019143:Evolution, Molecular; D020440:Gene Duplication; D020131:Genes, Duplicate; D006801:Humans; D010802:Phylogeny; D012984:Software
keywords: Gene duplication; Gene expression evolution; Neofunctionalization; Subfunctionalization