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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。
Objective To investigate the advantage of FastTree 2.1.8 for constructing a maximum likelihood tree using the pol gene fragment of HIV-1 as an example, and to provide a reference for the molecular phylogenetic studies of HIV-1 gene sequences. Methods All of the non-recombinant subtypes (A ~ D, F ~ H, J and K), CRF01_AE, BC recombination, 01B recombination, CRF65_cpx and SIVcpz as outgroups were selected from the subtype reference sequences of Los Alamos HIV Database The HIV-1 pol gene sequence was used as a research sample. The phylogenetic tree was constructed using the ML method of FastTree 2.1.8 and the ML of MEGA 6.06 and the adjacency method (NJ) respectively. Then, the phylogenetic tree of three phylogenetic trees Build time, accuracy, and branch support. Results FastTree 2.1.8 was the fastest (10.8 seconds), which was significantly better than that of MEGA 6.06 (70 767 seconds) and NJ (82 seconds). FastTree 2.1.8 ML tree was 94.0% with MEGA 6.06 ML (Χ ~ 2 = 1.401, P = 0.540). The nearest common ancestor node (MRCA) of two subtypes with three or more sequences on phylogenetic tree showed no significant difference There was no significant difference in branch support (χ ~ 2 = 1.057, P = 0.590). Conclusion FastTree, as a rapid phylogenetic tree software, is significantly superior to the commonly used MEGA 6.06 in tree construction time, making it possible to build a ML tree based on big data set on a personal computer. It is a molecular phylogenetic analysis of HIV-1 gene sequence A powerful tool in the field.