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Estimation of Gene Insertion/Deletion Rates with Missing Data.

ABSTRACT: Lateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modeled in a maximum-likelihood framework with the additional flexibility of modeling 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.

SUBMITTER: Dang UJ

PROVIDER: S-EPMC5068843 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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Estimation of Gene Insertion/Deletion Rates with Missing Data.

Dang Utkarsh J UJ Devault Alison M AM Mortimer Tatum D TD Pepperell Caitlin S CS Poinar Hendrik N HN Golding G Brian GB

Genetics 20160826 2

Lateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modeled in a maximum-likelihood framework with the additional flexibility of modeling 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 ill ...[more]

PMID: 27565162

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