Bonsai

Bonsai infers and assembles large pedigrees from genotype data to reconstruct familial relationships, including cases with sparsely sampled individuals and distant relatives.

Key Features:

• Pedigree Inference: Infers small pedigrees composed of close relatives and assembles them into larger, comprehensive family trees.
• Innovative Formulas and Tools: Implements novel formulas, including a likelihood model for determining the degree of separation between small pedigrees.
• Background IBD Detection: Identifies individuals who share background identity-by-descent (IBD) that does not indicate recent common ancestry.
• Ancestral Branch Identification: Detects ancestral branches through which distant relatives are connected.

Scientific Applications:

• Pedigree reconstruction: Reconstructing large and complex familial relationships in genetic research.
• Hereditary pattern analysis: Analyzing patterns of inheritance to study hereditary traits.
• Population genetics: Investigating population-level relatedness and structure.
• Related fields: Applications requiring inference of large pedigrees and distant relationships.

Methodology:

Integrates age information directly into likelihood calculations rather than using it solely for consistency checks, and employs a heuristic branch-and-bound-like approach to explore possible pedigree configurations efficiently.