Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0

Abstract

Summary: ArchaicSeeker 2.0 is designed to identify the sequences derived from known or unknown archaic hominins and to further model the multiple-wave gene flows. The main functional modules involve seeking introgressed sequences, determining corresponding ancestries, and reconstructing the admixture history. The protocol below describes the analytic steps for the application of ArchaicSeeker 2.0 into analysis of example data of the Han Chinese population.For complete details on the use and execution of this protocol, please refer to Yuan et al. (2021).

Keywords

• Bioinformatics
• Sequence analysis
• Genetics