Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0
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 admixtur...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-06-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722001940 |
| _version_ | 1818059133592535040 |
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| author | Rui Zhang Kai Yuan Shuhua Xu |
| author_facet | Rui Zhang Kai Yuan Shuhua Xu |
| author_sort | Rui Zhang |
| collection | DOAJ |
| description | 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). |
| first_indexed | 2024-12-10T13:11:41Z |
| format | Article |
| id | doaj.art-2b58fe479817443e8d8098c25d6f37b0 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-12-10T13:11:41Z |
| publishDate | 2022-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-2b58fe479817443e8d8098c25d6f37b02022-12-22T01:47:38ZengElsevierSTAR Protocols2666-16672022-06-0132101314Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0Rui Zhang0Kai Yuan1Shuhua Xu2Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, ChinaKey Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, ChinaState Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China; Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Corresponding authorSummary: 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).http://www.sciencedirect.com/science/article/pii/S2666166722001940BioinformaticsSequence analysisGenetics |
| spellingShingle | Rui Zhang Kai Yuan Shuhua Xu Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0 STAR Protocols Bioinformatics Sequence analysis Genetics |
| title | Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0 |
| title_full | Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0 |
| title_fullStr | Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0 |
| title_full_unstemmed | Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0 |
| title_short | Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0 |
| title_sort | detecting archaic introgression and modeling multiple wave admixture with archaicseeker 2 0 |
| topic | Bioinformatics Sequence analysis Genetics |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722001940 |
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