Estimation of gene insertion/deletion rates with missing data
Lateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modelled in a maximum likelihood framework with the additional flexibility of modelling potential missing data.
Aug 28, 2016
Authors: Utkarsh J. Dang, Alison M. Devault, Tatum D. Mortimer, Caitlin S. Pepperell, Hendrik N. Poinar, and G. Brian Golding
Genetics: Early Online, DOI: 10.1534/genetics.116.191973
Abstract
Lateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modelled in a maximum likelihood framework with the additional flexibility of modelling potential missing data. The performance of the models is illustrated using simulations and a data set on gene family phyletic patterns from Gardnerella vaginalis that includes an ancient taxon. A novel application involving pseudogenization/genome reduction magnitudes is also illustrated using gene family data from Mycobacterium spp. Finally, an R package called indelmiss is available from the Comprehensive R Archive Network at https://cran.r-project.org/package=indelmiss, with support documentation and examples.