Abstract Detail

Recent Topics Posters

Blischak, Paul [1], Wolfe, Andrea D. [2].

PPGtk: a software project for population genetics in polyploids.

Whole genome duplication is a common phenomenon in many plant lineages at both historical and contemporary time scales. As interest in polyploid research has grown, there has been a need for software/methods to analyze the large amounts genetic data that are being generated to study these taxa. However, it is often the case that there is little prior information regarding the evolutionary history of the polyploid species being studied. With this problem in mind, the polyploid pop-gen toolkit (PPGtk) aims to provide a low entry point for the analysis of biallelic SNP data collected in contemporary autopolyploids and allopolyploids by focusing on methods for non-model taxa. The tools we are currently developing use genotype likelihoods and simple demographic models to make inferences about genetic diversity, genotypes, and allele frequencies. The software is written in C++ and uses OpenMP for multithreading, allowing for faster computations with large SNP data sets. The source code for the project will be made available on GitHub and a precompiled version of the software will be made available for use with any operating system via a Docker image. The ultimate goal for PPGtk is to provide an easily accessible, open source suite of tools that continues to grow as new methods are developed.

1 - Ohio State University, Evolution, Ecology and Organismal Biology, 318 W. 12th Ave, Columbus, OH, 43210, USA
2 - Ohio State University, Department Of Ecology, Evolution, And Organismal Biology, 318 W. 12th Avenue, COLUMBUS, OH, 43210-1293, USA

Keywords:
polyploidy
Software
population genetics
statistical modeling.

Presentation Type: Recent Topics Poster
Session: P, Recent Topics Posters
Location: Exhibit Hall/Savannah International Trade and Convention Center
Date: Monday, August 1st, 2016
Time: 5:30 PM
Number: PRT019
Abstract ID:1214
Candidate for Awards:None