發(fā)布時間：2018-06-20 09:02

  本文選題：艾滋病病毒型 + FastTree..��； 參考：《中國艾滋病性病》2017年08期

【摘要】：目的以艾滋病病毒1型(HIV-1)的pol區(qū)基因片段為例,研究FastTree2.1.8構(gòu)建最大似然樹的優(yōu)勢所在,為HIV-1基因序列的分子系統(tǒng)發(fā)生學(xué)研究提供參考。方法通過從Los Alamos HIV Database的亞型參考序列中選擇全部非重組亞型(A~D、F~H、J和K)、CRF01_AE、BC重組、01B重組、CRF65_cpx和作為外群的SIVcpz共100條HIV-1 pol區(qū)基因序列作為研究樣本,分別應(yīng)用FastTree2.1.8的最大似然法(ML)和MEGA6.06的ML以及鄰接法(NJ)構(gòu)建系統(tǒng)進化樹,然后比較三個系統(tǒng)進化樹的構(gòu)建時間、準確性以及分支支持度之間的差別。結(jié)果 FastTree2.1.8的建樹時間最快(10.8秒),明顯優(yōu)于MEGA 6.06的ML法(70 767秒)和NJ法(82秒);FastTree2.1.8 ML樹的準確率為94.0%,MEGA 6.06 ML樹和NJ樹均為90.0%,三者差異無統(tǒng)計學(xué)意義(χ~2=1.401,P=0.540);三棵系統(tǒng)進化樹上具有兩個以上序列的亞型的最近共同祖先節(jié)點(MRCA)的分支支持度差異無統(tǒng)計學(xué)意義(χ~2=1.057,P=0.590)。結(jié)論 FastTree作為快速構(gòu)建系統(tǒng)進化樹的軟件,在建樹時間上明顯優(yōu)于常用的MEGA 6.06,使在個人電腦上構(gòu)建基于大數(shù)據(jù)集的ML樹成為可能,是HIV-1基因序列分子系統(tǒng)發(fā)生分析研究領(lǐng)域的一個有力工具。
[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.
【作者單位】： 廣東藥科大學(xué);廣州市疾病預(yù)防控制中心;
【分類號】：R373

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