Inference of Ancestral Recombination Graphs Using ARGweaver

Hubisz, M., Siepel, A. (January 2020) Inference of Ancestral Recombination Graphs Using ARGweaver. Methods Mol Biol, 2090. pp. 231-266. ISSN 1064-3745

Abstract

This chapter describes the usage of the program ARGweaver, which estimates the ancestral recombination graph for as many as about 100 genome sequences. The ancestral recombination graph is a detailed description of the coalescence and recombination events that define the relationships among the sampled sequences. This rich description is useful for a wide variety of population genetic analyses. We describe the preparation of data and major considerations for running ARGweaver, as well as the interpretation of results. We then demonstrate an analysis using the DARC (Duffy) gene as an example, and show how ARGweaver can be used to detect signatures of natural selection and Neandertal introgression, as well as to estimate the dates of mutation events. This chapter provides sufficient detail to get a new user up and running with this complex but powerful analysis tool.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > computational biology > algorithms bioinformatics > computational biology bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes bioinformatics > genomics and proteomics > genetics & nucleic acid processing > population genetics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > recombination bioinformatics > computational biology > statistical analysis
CSHL Authors:	Siepel, Adam
Communities:	CSHL labs > Siepel lab CSHL Cancer Center Program > Cancer Genetics and Genomics Program
Depositing User:	Adrian Gomez
Date:	24 January 2020
Date Deposited:	31 Jan 2020 19:01
Last Modified:	30 Jan 2024 20:57
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/38946

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