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Title: A MANUAL FOR USE OF PYPEDAL: A SOFTWARE PACKAGE FOR PEDIGREE ANALYSIS

Author
item Cole, John

Submitted to: Software and User Manual Public Release
Publication Type: Book / Chapter
Publication Acceptance Date: 11/29/2005
Publication Date: 11/29/2005
Citation: Cole, J.B. 2005. A Manual for Use of Pypedal: a Software Package for Pedigree Analysis. Software and User Manual Public Release 2.0.0b15.

Interpretive Summary: This manual in eleven chapters describes PyPedal (v 2.0), a software package 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; this language may be used to easily automate analyses and implement new features. Input and output files utilize plain-text formats. The program has been used for the analysis of dairy cattle and working dog pedigrees. PyPedal runs on the GNU/Linux and Microsoft Windows operating systems. The program, documentation, and examples of usage are available at http://pypedal.sourceforge.net/.

Technical Abstract: This manual in eleven chapters describes PyPedal (v 2.0), a software package 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; this language may be used to easily automate analyses and implement new features. Input and output files utilize plain-text formats. The program has been used for the analysis of dairy cattle and working dog pedigrees. PyPedal runs on the GNU/Linux and Microsoft Windows operating systems. The program, documentation, and examples of usage are available at http://pypedal.sourceforge.net/.