植物群体遗传进化研究方法探析  

Exploring the algorithms of plant population genetics and evolution

作　　者：郎娜[1] 刘之慧[1] 宋艰难 董清华[1] 

机构地区：[1]北京农学院植物科学技术学院,北京102206

出　　处：《北京农学院学报》2016年第2期5-9,共5页Journal of Beijing University of Agriculture

基　　金：2015人才培养质量提高项目(就业与创业)"研究生创新科研项目"(5056516002/016);北京市属高等学校创新团队建设与教师职业发展计划项目(IDHT20140509)

摘　　要：【目的】评估植物群体遗传进化研究涉及的相关算法软件,为该研究领域提供方法选择参考。【方法】利用重测序数据,就群体遗传进化研究的各种算法做比较,对相关算法分析效果做对比评估。【结果】评估结果表明,进化树耗时和数据大小、模型选择均有较大关系,两者共同决定运算时间,另外运算效果还和多序列的比对效果有很大关系。群体结构分析fast Structure、Admixture软件运算速率、准确度较Structure软件有明显提高。主成分分析耗时相对较少,可用Cluster和R软件实现,两款软件的计算结果可相互验证;连锁不平衡分析推荐Plink2软件。【结论】算法及软件的选择对植物群体遗传进化研究的效率、结果影响较大。【Objective】In this study,we evaluated the algorithms and softwares of plant population genetics and evolution. And it will provide a new method for this research field.【Methods】In order to assess different methods,we compared and summarized a number of population genetic algorithms using the resequencing data. 【Results】The result showed that the time cost of the phylogenetic trees is largely depended on the model selection and data size,two of which collaboratively determined the running time. In addition,there is a great relationship between operation effect and multiple sequence alignment effect The software fast Structure of Group structure analysis,software Admixture of Operation rate and degree of accuracy are much better than Structure. ITheprinciple component analysis,which could be performed by the software of Cluster and R,spends less time. The calculation results of two softwares could be mutually verified. Plink2 software was recommended for linkage disequilibrium analysis. 【Conclusion】The choice of algorithms and softwares have a great effect on the efficiency and outcomes of the plant population genetic research.

关 键 词：群体进化 遗传 软件 算法 

分 类 号：Q347[生物学—遗传学]