Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0
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Published on: September 27, 2024
Rui Zhang1, Kai Yuan1, Shuhua Xu2,3,4
1Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
Abstract:
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).
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