HIV-TRAnsmission Cluster Engine (HIV-TRACE) and Cluster Picker are some of the most widely used programs for identifying HIV-1 transmission networks from nucleotide sequences. However, choosing between these tools is subjective and often a matter of personal preference. Because these software use different algorithms to detect HIV-1 transmission networks, their optimal use is better suited with different sequence data sets and under different scenarios. The performance of these tools has previously been evaluated across a range of genetic distance thresholds without an assessment of the differences in the structure of networks identified. In this study, we tested both programs on the same HIV-1 pol sequence data set (n = 2,017) from three Ugandan populations to examine their performance across different risk groups and evaluate the structure of networks identified. HIV-TRACE that uses a single-linkage algorithm identified more nodes in the same networks that were connected by sparse links than Cluster Picker. This suggests that the choice of the program used for identifying networks should depend on the study aims, the characteristics of the population being investigated, dynamics of the epidemic, sampling design, and the nature of research questions being addressed for optimum results. HIV-TRACE could be more applicable with larger data sets where the aim is to identify larger clusters that represent distinct transmission chains and in more diverse populations where infection has occurred over a period of time. In contrast, Cluster Picker is applicable in situations where more closely connected clusters are expected in the studied populations.

中文翻译：

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选择正确的程序从不同人群采样的核苷酸序列中识别 HIV-1 传播网络。

HIV-TRAnsmission Cluster Engine (HIV-TRACE) 和 Cluster Picker 是一些最广泛使用的程序，用于从核苷酸序列识别 HIV-1 传播网络。然而，在这些工具之间进行选择是主观的，通常是个人喜好的问题。由于这些软件使用不同的算法来检测 HIV-1 传播网络，因此它们的最佳使用更适合不同的序列数据集和不同的场景。这些工具的性能之前已经在一系列遗传距离阈值范围内进行了评估，而没有评估所识别网络结构的差异。在这项研究中，我们在相同的 HIV-1 pol序列数据集（n = 2,017) 来自三个乌干达人群，以检查他们在不同风险组中的表现并评估确定的网络结构。使用单链接算法的 HIV-TRACE 比 Cluster Picker 识别出相同网络中通过稀疏链接连接的更多节点。这表明用于识别网络的程序的选择应取决于研究目标、被调查人群的特征、流行动态、抽样设计以及为获得最佳结果而解决的研究问题的性质。HIV-TRACE 可能更适用于更大的数据集，其目的是确定代表不同传播链的更大集群，以及在一段时间内发生感染的更多样化人群。相比之下，