PyPop update - a software pipeline for large-scale multilocus population genomics
PyPop update - a software pipeline for large-scale multilocus population genomics
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DOI：
10.1111/j.1399-0039.2006.00769.x
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发表时间：
2007-04-01
期刊：
影响因子：
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通讯作者：
Thomson, G.
中科院分区：
文献类型：
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作者：
Lancaster, A. K.;Single, R. M.;Thomson, G.
来自多位点基因数据的群体遗传统计数据帮助我们了解遗传变异的模式及其对进化研究，特别是对人类疾病研究的影响。在任何给定的群体中，人们都可以估计单倍型频率，识别偏离Hardy-Weinberg平衡的情况，测试平衡或定向选择，并调查连锁不平衡的模式。现有的软件包主要面向按人口计算这类统计数字，而不是人口之间的比较和不同统计数字之间的比较。我们开发了PyPop(用于种群基因组学的Python)，以促进跨种群的种群遗传统计分析，以及种群内和种群间不同统计之间的关系。PyPop是一个开放源码的框架，用于对多位点基因数据进行大规模的群体遗传分析。除其他外，它还计算上述统计数据。PyPop部署了标准的可扩展标记语言(XML)输出格式，并可以将在不同时间对不同人群执行的多个分析的结果集成到可以读取到电子表格中的通用输出格式中。XML输出格式允许将PyPop作为更大的分析管道的一部分嵌入。PyPop最初是为了分析人类基因组中人类白细胞抗原区域的高度多态的遗传数据而开发的，它适用于任何类型的多位点遗传数据。它是分析第13届和第14届国际组织相容性讲习班人类学部分收集的数据的主要分析平台。PyPop还成功地用于我们团队与合作者的研究，以及几个独立研究团队的出版物中。
Population genetic statistics from multilocus genotype data inform our understanding of the patterns of genetic variation and their implications for evolutionary studies, generally, and human disease studies in particular. In any given population one can estimate haplotype frequencies, identify deviation from Hardy-Weinberg equilibrium, test for balancing or directional selection, and investigate patterns of linkage disequilibrium. Existing software packages are oriented primarily toward the computation of such statistics on a population-by-population basis, not on comparisons among populations and across different statistics. We developed PyPop (Python for Population Genomics) to facilitate the analyses of population genetic statistics across populations and the relationships among different statistics within and across populations. PyPop is an open-source framework for performing large-scale population genetic analyses on multilocus genotype data. It computes the statistics described above, among others. PyPop deploys a standard Extensible Markup Language (XML) output format and can integrate the results of multiple analyses on various populations that were performed at different times into a common output format that can be read into a spreadsheet. The XML output format allows PyPop to be embedded as part of a larger analysis pipeline. Originally developed to analyze the highly polymorphic genetic data of the human leukocyte antigen region of the human genome, PyPop has applicability to any kind of multilocus genetic data. It is the primary analysis platform for analyzing data collected for the Anthropological component of the 13th and 14th International Histocompatibility Workshops. PyPop has also been successfully used in studies by our group, with collaborators, and in publications by several independent research teams.