sstar: A Python']Python Package for Detecting Archaic Introgression from Population Genetic Data with S*

被引：3
|
作者：
Huang, Xin [1 ,2 ]
Kruisz, Patricia [3 ]
Kuhlwilm, Martin [1 ,2 ]
机构：
[1] Univ Vienna, Dept Evolutionary Anthropol, Djerassiplatz 1, A-1030 Vienna, Austria
[2] Univ Vienna, Human Evolut & Archaeol Sci HEAS, Djerassiplatz 1, A-1030 Vienna, Austria
[3] Univ Appl Sci Wiener Neustadt, Fac Engn, Dept Bio Data Sci, Biotech Campus Tulln,Konrad Lorenz Str 10, A-3430 Tulln, Austria
来源：
MOLECULAR BIOLOGY AND EVOLUTION | 2022年 / 39卷 / 11期
关键词：
introgression; archaic admixture; S*; !text type='Python']Python[!/text; NEANDERTHAL;
D O I：
10.1093/molbev/msac212
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
S* is a widely used statistic for detecting archaic admixture from population genetic data. Previous studies used freezing-archer to apply S*, which is only directly applicable to the specific case of Neanderthal and Denisovan introgression in Papuans. Here, we implemented sstar for a more general purpose. Compared with several tools, including SPrime, SkovHMM, and ArchaicSeeker2.0, for detecting introgressed fragments with simulations, our results suggest that sstar is robust to differences in demographic models, including ghost introgression and two-source introgression. We believe sstar will be a useful tool for detecting introgressed fragments in various scenarios and in non-human species.
引用
收藏
页数：4
相关论文
共 50 条
  • [21] ColiCoords: A Python']Python package for the analysis of bacterial fluorescence microscopy data
    Smit, Jochem H.
    Li, Yichen
    Warszawik, Eliza M.
    Herrmann, Andreas
    Cordes, Thorben
    PLOS ONE, 2019, 14 (06):
  • [22] A Python']Python Package for the Localization of Protein Modifications in Mass Spectrometry Data
    Barente, Anthony S.
    Villen, Judit
    JOURNAL OF PROTEOME RESEARCH, 2022, : 501 - 507
  • [23] Enhancements to Ginga: a Python']Python Package for Building Astronomical Data Viewers
    Jeschke, Eric
    Inagaki, Takeshi
    Kackley, Russell
    ASTRONOMICAL DATA ANALYSIS SOFTWARE AND SYSTEMS: XXIV, 2015, 495 : 169 - 172
  • [24] pyPMU - Open Source Python']Python Package for Synchrophasor Data Transfer
    Sandi, Stevan
    Krstajic, Bozo
    Popovic, Tomo
    2016 24TH TELECOMMUNICATIONS FORUM (TELFOR), 2016, : 861 - 864
  • [25] GeospaceLAB: Python']Python package for managing and visualizing data in space physics
    Cai, Lei
    Aikio, Anita
    Kullen, Anita
    Deng, Yue
    Zhang, Yongliang
    Zhang, Shun-Rong
    Virtanen, Ilkka
    Vanhamaki, Heikki
    FRONTIERS IN ASTRONOMY AND SPACE SCIENCES, 2022, 9
  • [26] scikit-fda: A Python']Python Package for Functional Data Analysis
    Ramos-Carreno, Carlos
    Carbajo-Berrocal, Miguel
    Torrecilla, Jose Luis
    Marcos, Pablo
    Suarez, Alberto
    JOURNAL OF STATISTICAL SOFTWARE, 2024, 109 (02): : 1 - 37
  • [27] Genetic diversity and population genetic structure of Python']Python bivittatus in China
    Duan, Yubao
    Wang, Yingshu
    Bai, Suying
    Tian, Xiuhua
    Rong, Ke
    Ma, Jianzhang
    JOURNAL OF FORESTRY RESEARCH, 2017, 28 (03) : 621 - 628
  • [28] MSIFinder: a python']python package for detecting MSI status using random forest classifier
    Zhou, Tao
    Chen, Libin
    Guo, Jing
    Zhang, Mengmeng
    Zhang, Yanrui
    Cao, Shanbo
    Lou, Feng
    Wang, Haijun
    BMC BIOINFORMATICS, 2021, 22 (01)
  • [29] Systems Neuroscience Computing in Python']Python (SyNCoPy): a python']python package for large-scale analysis of electrophysiological data
    Moenke, Gregor
    Schaefer, Tim
    Parto-Dezfouli, Mohsen
    Kajal, Diljit Singh
    Fuertinger, Stefan
    Schmiedt, Joscha Tapani
    Fries, Pascal
    FRONTIERS IN NEUROINFORMATICS, 2024, 18
  • [30] NeuTomPy toolbox, a Python']Python package for tomographic data processing and reconstruction
    Micieli, Davide
    Minniti, Triestino
    Gorini, Giuseppe
    SOFTWAREX, 2019, 9 : 260 - 264
12345