AngelPedTK– An efficient toolkit for comprehensive animal pedigree management

Mahboob Al¹ Mi Na Park ¹ Chang Gwon Dang ¹ Sidong Kim ^1,*

¹Animal Breeding and Genetics Division, National Institute of Animal Science

Abstract

Acquiring an accurate raw pedigree for animal genetic analyses is a challenging task. The sources of errors are mostly personnel or farmers who manage pedigree information. To date, many softwares are found for animal breeding research featuring faster and advanced algorithms for animal data analyses. However, these softwares are deemed incomplete or lack proper functionalities, especially for comprehensive pedigree handling. We, therefore, developed a suit software packages namely AngelPedTK (Animal Genetic Evaluation Laboratory Pedigree Toolkit) version 1.0 to support a comprehensive pedigree management and enhance the user-experience while being computation efficient. AngelPedTK is collection of four base modules– PedCheck (to check pedigree errors), PedTrace (to create a sub-pedigree which contains animals for the analysis from whole pedigree), PedStack (to prune pedigree and generate a chronologically ordered pedigree such that parents appear before their progeny), and PedGetF (to calculate numerator relationship matrix (NRM), inbreeding coefficient and pedigree completeness index). This toolkit includes both command-line interface and a graphical user interface (GUI). The core modules are written in low-level C language enabling faster data processing. The GUI front end is a wrapper module built on top of the core modules to provide a flexible working environment. Although implementation of GUI, which most available softwares limits, comes at a cost of memory usage or a little processing expense, yet a good balance is maintained due to the deployment of efficient algorithm. We hope that this software will assist a large range of users through user-friendly features and processing comprehensiveness.

Acknowledgements

This research was supported by the funding from the project “Development of Estimation Model for Hanwoo Breeding Value and Accuracy Improvement of Genetic Merit Evaluation (Project No: PJ01260602)” and the “RDA Research Associate Fellowship Program” of the National Institute of Animal Science, Cheonan, Korea.

Figures & Tables

The main fornt-end GUI of AngelPedTk.