Bridging Trees for Posterior Inference on Ancestral Recombination Graphs

Overview

Journal Proc Math Phys Eng Sci

Date 2019 Jan 4

PMID 30602937

Citations 9

Authors

K Heine

A Beskos

A Jasra

D Balding

M De Iorio

Affiliations

Soon will be listed here.

Abstract

We present a new Markov chain Monte Carlo algorithm, implemented in the software Arbores, for inferring the history of a sample of DNA sequences. Our principal innovation is a bridging procedure, previously applied only for simple stochastic processes, in which the local computations within a bridge can proceed independently of the rest of the DNA sequence, facilitating large-scale parallelization.

Citing Articles

Inference and applications of ancestral recombination graphs.

Nielsen R, Vaughn A, Deng Y Nat Rev Genet. 2024; 26(1):47-58.

PMID: 39349760 DOI: 10.1038/s41576-024-00772-4.

A general and efficient representation of ancestral recombination graphs.

Wong Y, Ignatieva A, Koskela J, Gorjanc G, Wohns A, Kelleher J Genetics. 2024; 228(1).

PMID: 39013109 PMC: 11373519. DOI: 10.1093/genetics/iyae100.

The Promise of Inferring the Past Using the Ancestral Recombination Graph.

Brandt D, Huber C, Chiang C, Ortega-Del Vecchyo D Genome Biol Evol. 2024; 16(2).

PMID: 38242694 PMC: 10834162. DOI: 10.1093/gbe/evae005.

The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics.

Lewanski A, Grundler M, Bradburd G PLoS Genet. 2024; 20(1):e1011110.

PMID: 38236805 PMC: 10796009. DOI: 10.1371/journal.pgen.1011110.

A general and efficient representation of ancestral recombination graphs.

Wong Y, Ignatieva A, Koskela J, Gorjanc G, Wohns A, Kelleher J bioRxiv. 2023; .

PMID: 37961279 PMC: 10635123. DOI: 10.1101/2023.11.03.565466.

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