lineagekit

A python library with genealogy methods. We will seek to integrate code or functionality or both from:

ISGEN (Dominic's code on importance sampling)

https://github.com/DomNelson/ISGen

Earlier iterations of genealogy alignment project:

Useful data structures built on top of networkx:

• Genealogical: Generic data structure that includes implementation of useful functions on geneological objects (trees, pedigrees, etc.).
• Pedigree
  • Implements Lange's Kinship estimation algorithm with sparse matrices (may need to be optimized)
• HaplotypeGraph: Converts from a pedigree to a graph encompassing all potential inheritance paths.
  • Supports autosomal, X, Y, and mitochondrial inheritance paths.
  • Has a (non-tested) message passing algorithm for computing kinship.
• Traversal (corresponds to trees)

https://github.com/ivan-krukov/aligning-genealogies/tree/master/genealogy_aligner

genlib (Marie-Hélène Roy-Gagnon's R pacakge.

Andrii's aligner

Luke pedigree simulations

sgkit