Given a group of genomes, represented as the sets of genes that belong to them, the discovery of the pangenomic content is based on the search of genetic homology among the genes for clustering them into families. Thus, pangenomic analyses investigate the membership of the families to the given genomes. This approach is referred to as the gene-oriented approach in contrast to other definitions of the problem that takes into account different genomic features. In the past years, several tools have been developed to discover and analyse pangenomic contents. Because of the hardness of the problem, each tool applies a different strategy for discovering the pangenomic content. This results in a differentiation of the performance of each tool that depends on the composition of the input genomes. This review reports the main analysis instruments provided by the current state of the art tools for the discovery of pangenomic contents. Moreover, unlike previous works, the presented study compares pangenomic tools from a methodological perspective, analysing the causes that lead a given methodology to outperform other tools. The analysis is performed by taking into account different bacterial populations, which are synthetically generated by changing evolutionary parameters. The benchmarks used to compare the pangenomic tools, in addition to the computational pipeline developed for this purpose, are available at https://github.com/InfOmics/pangenes-review. Contact: V. Bonnici, R. Giugno Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.

中文翻译：

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以基因为导向的泛基因组内容发现方法面临的挑战。

给定一组基因组，表示为属于它们的一组基因，泛基因组内容的发现基于对基因之间的遗传同源性的搜索，以便将它们聚类成家族。因此，泛基因组分析调查给定基因组的家族成员。与考虑不同基因组特征的问题的其他定义相比，这种方法被称为面向基因的方法。在过去的几年中，已经开发了多种工具来发现和分析泛基因组内容。由于问题的难度，每个工具都采用不同的策略来发现泛基因组内容。这导致每个工具的性能有所不同，这取决于输入基因组的组成。本综述报告了当前最先进的工具提供的主要分析工具，用于发现泛基因组内容。此外，与以前的工作不同，本研究从方法论的角度比较了泛基因组工具，分析了导致给定方法优于其他工具的原因。该分析是通过考虑不同的细菌种群来进行的，这些细菌种群是通过改变进化参数合成的。用于比较泛基因组工具的基准，以及为此目的开发的计算管道，可在 https://github.com/InfoOmics/pangenes-review 获得。本研究从方法论的角度比较泛基因组工具，分析导致特定方法优于其他工具的原因。该分析是通过考虑不同的细菌种群来进行的，这些细菌种群是通过改变进化参数合成的。用于比较泛基因组工具的基准，以及为此目的开发的计算管道，可在 https://github.com/InfoOmics/pangenes-review 获得。本研究从方法论的角度比较泛基因组工具，分析导致特定方法优于其他工具的原因。该分析是通过考虑不同的细菌种群来进行的，这些细菌种群是通过改变进化参数合成的。用于比较泛基因组工具的基准，以及为此目的开发的计算管道，可在 https://github.com/InfoOmics/pangenes-review 获得。联系人： V. Bonnici, R. Giugno补充信息：补充数据可在在线生物信息学简报中获得。