1.1 Features

Some of the notable features of PyPedal include:

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 () 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 tabulat method [Lacy, Alaks, and WalshLacy et al.1996,Gulisija, Gianola, Weigel, and ToroGulisija et al.2006];
Calculation of coefficients of ancestral inbreeding using the methods of Ballou Ballou1997 or Suwanlee et al. SuwanleeBSC2007;
Decomposition of into and such that ;
Computation of the direct inverse of (not accounting for inbreeding) using the method of Henderson ref143;
Computation of the direct inverse of (accounting for inbreeding) using the method of Quaas ref235;
Storage of and its inverse between user sessions as persistent Python objects using the pickle module to avoid unnecessary calculations;
Calculation of theoretical and actual effective population sizes;
Computation of effective founder number using the exact algorithm of Lacy ref640;
Computation of effective founder number using the approximate algorithm of Boichard et al. ref352;
Computation of effective ancestor number using the algorithms of Boichard et al. ref352;
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;
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;

PyPedal has been used to perform calculations on pedigrees as large as 600,000 animals and has been used in scientific research [Cole, Franke, and LeightonCole et al.2004,ColeCole2007].

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