Visualising errors in animal pedigree genotype data
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PyPedal is a pedigree analysis package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization. A number of measures of genetic variability are provided, including coefficients of inbreeding and relationship, effective founder and ancestor numbers, and founder genome equivalents. Routines are also included for identifying ancestors and descendants, computing coefficients of inbreeding from potential matings, quantifying pedigree completeness, visualizing pedigrees, and producing high-quality printed reports. In addition, a module is provided for applying graph theoretic tools to pedigrees. Input and output files utilize plain-text formats, and printed reports are rendered as Adobe PDF files. Users can easily write programs for automating analyses as well as create new reports. PyPedal has been validated using dairy cattle and working dog pedigrees. It is written in the Python programming language and operates on a number of operating systems, including GNU/Linux and Microsoft Windows. The program is free of charge; code, documentation, and examples of usage are available at http://pypedal.sourceforge.net/.