PyPedal

Features

• Reading pedigree files in user-defined formats
• Checking pedigree integrity (duplicate IDs, parents younger than offspring, etc.)
• Generating summary information such as frequency of appearance in the pedigree file
• Reordering and renumbering of pedigree files
• Computation of the numerator relationship matrix (A) from a pedigree file using the tabular method
• Inbreeding calculations for large pedigrees
• Computation of average total and average individual coefficients of inbreeding and relationship
• Calculation of coefficients of partial inbreeding using an iterative tabular method (Lacy, 1996; Gulisija, 2006)
• Calculation of coefficients of ancestral inbreeding using the methods of Ballou (1997) or Suwanlee et al. (2007)
• Calculation of theoretical and actual effective population sizes
• Computation of effective founder number using the exact algorithm of Lacy
• Computation of effective founder number using the approximate algorithm of Boichard et al.
• Computation of effective ancestor number using the algorithms of Boichard et al.
• Selection of subpedigrees containing all ancestors of an animal
• Identification of the common relatives of two animals
• Calculation of the inbreeding of offspring from a prospective mating
• Output to ASCII text files, including matrices, coefficients of inbreeding and relationship, and summary information
• Importation and exportation of GEDCOM 5.5 files
• Importation and exportation of GENES 1.20 (dBase III) files
• Loading pedigrees from, and saving them to, MySQL, Postgres, and SQLite databases
• Simulation of pedigrees using an algorithm derived from that in Matvec 1.1a

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