Submitted to: Computers and Electronics in Agriculture
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 8, 2007
Publication Date: April 2, 2007
Citation: Cole, J.B. 2007. Pypedal: A computer program for pedigree analysis. Computers and Electronics in Agriculture. 57:107-113.
Interpretive Summary: Applications for pedigree analysis are often challenging for non-technical users,limited to single operating systems, expensive, or not easily extensible. PyPedal is crossplatform, free, and extensible. It runs on the GNU/Linux and Microsoft Windows operating systems and is available online at http://pypedal.sourceforge.net/. It provides many pedigree metrics, visualization tools, and reporting functions. Scripting uses the Python programming language and is used to automate analyses and implement new features. Input and output files utilize plain-text formats. PyPedal has been applied to the pedigrees for a colony of dog guides and the U.S. Ayrshire population.
The objective of this paper is to describe the program PyPedal (v 2.0) and provide computational details for some of its key metrics. The package provides tools for pedigree analysis, report generation, and data visualization. Metrics include coefficients of inbreeding and relationship, effective founder and ancestor numbers, and founder genome equivalents. Tools are provided for identifying ancestors and descendants, computing coefficients of inbreeding from potential matings, quantifying pedigree completeness, and visualizing pedigrees. Scripting support is provided by the Python programming language and may be used to easily automate analyses and implement new features. Input and output files utilize plain-text formats. PyPedal runs on the GNU/Linux and Microsoft Windows operating systems. The program, documentation, and examples of usage are available on the World Wide Web at http://pypedal.sourceforge.net/. PyPedal has been applied to the pedigrees for a colony of dog guides and the U.S. Ayrshire population.