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PyPedal

Posted on by Robin Ding Leave a comment Information Analysis, Mathematics
5.0

PyPedal is a Python module that provides tools for the manipulation of pedigrees, simple visualization of pedigrees, and the calculation of measures of genetic diversity from pedigrees.

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Website http://pypedal.sourceforge.net
Tags
License GNU Library or Lesser General Public License version 2.0 (LGPLv2)
Platform BSD Linux Windows
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