About PyPedal
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. Features Reading pedigree files in...
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.
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
Previous Versions
Here you can find the changelog of PyPedal since it was posted on our website on 2015-04-26 03:00:00.
The latest version is 2.0.0 and it was updated on 2024-04-22 10:06:56. See below the changes in each version.
PyPedal version 2.0.0
Updated At: 2012-05-15
PyPedal version 2.0.1
Updated At: 2010-12-30
Changes: Several fixes and updates
Disclaimer
External Download
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