Download

PyPedal is designed as Python module that is supposed to provide instruments for the manipulation of pedigrees. The tools provided can also offer simple visualization of pedigrees and the calculation of measures of genetic diversity from pedigrees.

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