应用FastTree2.1.8快速构建HIV-1 pol区基因的最大似然系统进化树

发布时间：2018-06-20 09:02

本文选题：艾滋病病毒型 + FastTree..　；参考：《中国艾滋病性病》2017年08期

【摘要】：目的以艾滋病病毒1型(HIV-1)的pol区基因片段为例,研究FastTree2.1.8构建最大似然树的优势所在,为HIV-1基因序列的分子系统发生学研究提供参考。方法通过从Los Alamos HIV Database的亚型参考序列中选择全部非重组亚型(A~D、F~H、J和K)、CRF01_AE、BC重组、01B重组、CRF65_cpx和作为外群的SIVcpz共100条HIV-1 pol区基因序列作为研究样本,分别应用FastTree2.1.8的最大似然法(ML)和MEGA6.06的ML以及邻接法(NJ)构建系统进化树,然后比较三个系统进化树的构建时间、准确性以及分支支持度之间的差别。结果 FastTree2.1.8的建树时间最快(10.8秒),明显优于MEGA 6.06的ML法(70 767秒)和NJ法(82秒);FastTree2.1.8 ML树的准确率为94.0%,MEGA 6.06 ML树和NJ树均为90.0%,三者差异无统计学意义(χ~2=1.401,P=0.540);三棵系统进化树上具有两个以上序列的亚型的最近共同祖先节点(MRCA)的分支支持度差异无统计学意义(χ~2=1.057,P=0.590)。结论 FastTree作为快速构建系统进化树的软件,在建树时间上明显优于常用的MEGA 6.06,使在个人电脑上构建基于大数据集的ML树成为可能,是HIV-1基因序列分子系统发生分析研究领域的一个有力工具。
[Abstract]:Objective to study the advantages of constructing the maximum likelihood tree (MLT) in pol region of HIV-1 (HIV-1), and to provide a reference for the molecular phylogeny of HIV-1 gene sequence. Methods A total of 100 HIV-1 pol gene sequences were selected from the reference sequences of Los Alamos Database subtypes. MLM of Fast Tree 2.1.8 and ML of MEGA 6.06 and NJ) of MEGA 6.06 were used to construct phylogenetic tree, and then the differences among the time, accuracy and branch support of the three tree were compared. Results the construction time of FastTree 2.1.8 was the fastest (10.8 seconds), which was significantly better than that of Mega 6.06 (ML method 70 767 seconds) and NJ (82 seconds FastTree 2.1.8 ML tree). The accuracy rate of FastTree 2.1.8 ML tree was 94.0 0. 0% and 90.0% of MEGA 6.06 ML tree and NJ tree respectively. There was no significant difference among the three trees (蠂 2, 1. 401) and three phylogenetic trees. There was no significant difference in branch support of the most recent common ancestor node MRCA with more than two subtypes (蠂 ~ 2 ~ 2 ~ (1.057) P ~ (0.590). Conclusion FastTree, as a fast software for constructing phylogenetic tree, is better than Mega 6.06in building time, which makes it possible to construct ML tree based on big data set on personal computer. It is a powerful tool in the field of molecular phylogenetic analysis of HIV-1 gene sequence.
【作者单位】：广东药科大学;广州市疾病预防控制中心;
【分类号】：R373

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