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.
- 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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Excellent programs, latest code can be found on Github github.com/wintermind/pypedal
Pypedal is excellent! Thanks.