Submitted to: Python Magazine
Publication Type: Popular Publication
Publication Acceptance Date: December 31, 2008
Publication Date: March 30, 2009
Citation: Cole, J.B. 2009. Using Python for Pedigree Analysis. Python Magazine. 3(3):12-20.
A pedigree is a way of describing a population of people or animals in terms of genetic relationships among individuals. Pedigrees are of interest to many people, including scientists, animal and plant breeders, and genealogists. They are used to assess the diversity of populations, in combination with performance records in genetic evaluation programs, and to trace the inheritance of beneficial or harmful alleles in a population. PyPedal is a software package for pedigree analysis that is designed as a standalone package that can easily be scripted. The Python programming language was used because of its support for procedural and object-oriented programming paradigms, its rich data structures, the availability of third-party libraries, speed of development, and support for the Linux operating system. PyPedal performs well on pedigrees of hundreds to thousands of animals, and is capable of processing pedigrees of hundreds-of-thousands or millions of records.