A forest is more than its trees: haplotypes and inferred ARGs DOI Creative Commons
Halley Fritze, Nathaniel S. Pope, Jerome Kelleher

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 2, 2024

Foreshadowing haplotype-based methods of the genomics era, it is an old observation that "junction" between two distinct haplotypes produced by recombination inherited as a Mendelian marker. In genealogical context, this recombination-mediated information reflects persistence ancestral across local trees in which they do not represent coalescences. We show how these non-coalescing ("locally-unary nodes") may be inserted into graphs (ARGs), compact but information-rich data structure describing relationships among recombinant sequences. The resulting ARGs are smaller, faster to compute with, and additional nearly always correct where initial ARG correct. provide efficient algorithms infer locally-unary nodes within existing ARGs, explore some consequences for inferred from real data. To this, we introduce new metrics agreement disagreement that, unlike previous methods, consider rather than just collection trees.

Language: Английский

Inference and applications of ancestral recombination graphs DOI
Rasmus Nielsen, Andrew H. Vaughn, Yun Deng

et al.

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 30, 2024

Language: Английский

Citations

14
A general and efficient representation of ancestral recombination graphs DOI Creative Commons
Yan Wong, Anastasia Ignatieva, Jere Koskela

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 4, 2023

Abstract As a result of recombination, adjacent nucleotides can have different paths genetic inheritance and therefore the genealogical trees for sample DNA sequences vary along genome. The structure capturing details these intricately interwoven is referred to as an ancestral recombination graph (ARG). Classical formalisms focused on mapping coalescence events nodes in ARG. This approach out step with modern developments, which do not represent terms or explicitly infer them. We present simple formalism that defines ARG specific genomes their intervals inheritance, show how it generalises classical treatments encompasses outputs recent methods. discuss nuances arising from this more general structure, argue forms appropriate basis software standard rapidly growing field.

Language: Английский

Citations

15
A forest is more than its trees: haplotypes and inferred ARGs DOI Creative Commons
Halley Fritze, Nathaniel S. Pope, Jerome Kelleher

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 2, 2024

Foreshadowing haplotype-based methods of the genomics era, it is an old observation that "junction" between two distinct haplotypes produced by recombination inherited as a Mendelian marker. In genealogical context, this recombination-mediated information reflects persistence ancestral across local trees in which they do not represent coalescences. We show how these non-coalescing ("locally-unary nodes") may be inserted into graphs (ARGs), compact but information-rich data structure describing relationships among recombinant sequences. The resulting ARGs are smaller, faster to compute with, and additional nearly always correct where initial ARG correct. provide efficient algorithms infer locally-unary nodes within existing ARGs, explore some consequences for inferred from real data. To this, we introduce new metrics agreement disagreement that, unlike previous methods, consider rather than just collection trees.

Language: Английский

Citations

1