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
Modern C++, standards-compliant with enhanced language extensions, beautiful native UI tools, and cross-compilation to Windows, macOS, iOS and Android. We provide the ‘full stack’ for native app development, from database to native and flexible UI to REST and more. If you want crossplatform C++ done right - choose the Complete App Platform for Multi-Device Native Development - Choose C++Builder.
Rate This ProjectLogin To Rate This Project
There are no 3 star reviews.