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HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching

机译：HomBlocks：基于局部共线块搜索的细胞器系统发育学多路线构建管道

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Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multiple sequence alignment. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multiple sequence alignment in a few hours. In addition, HomBlocks supports organelle genomes without annotation and makes adjustment to different taxon datasets, thereby enabling the inclusion of as many common genes as possible. Topology comparison of trees built by conventional multi-gene and HomBlocks alignments implemented in different taxon categories shows that the same efficiency can be achieved by HomBlocks as when using the traditional method. The availability of Homblocks makes organelle phylogenetic analyses more accessible to non-bioinformaticians, thereby promising to lead to a better understanding of phylogenic relationships at an organelle genome level.
机译：细胞器系统学分析需要精确构建的多基因比对矩阵，该矩阵由预先比对的单基因数据集连接而成。对于非生物信息学家，手动创建包含数十或数百个同源基因的高质量多基因比对可能需要几天甚至几周的时间。在这里，我们描述了一种新的高效管道HomBlocks，它使用同源块搜索方法构建多序列比对。这种方法可以自动识别细胞器基因组之间的局部共线块，并在几个小时内挖掘系统发育信息区域，以构建多个序列比对。此外，HomBlocks支持细胞器基因组而无需注释，并可以调整不同的分类单元数据集，从而可以包含尽可能多的常见基因。由传统的多基因和在不同分类单元中实现的HomBlocks比对构建的树木的拓扑比较显示，HomBlocks可以实现与使用传统方法时相同的效率。 Homblocks的可用性使非生物信息学家更容易进行细胞器系统发育分析，从而有望在细胞器基因组水平上更好地理解系统发生关系。

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