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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核科学的多对准结构管道

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Abstract 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. Availability and implementation HomBlocks is implemented in Perl and is supported by Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download from https://github.com/fenghen360/HomBlocks.git , and documentation and tutorials are available at https://github.com/fenghen360/HomBlocks . Contact: yxmao@ouc.edu.cn or fenghen360@126.com Highlights ? HomBlocks is a highly efficient and easy-to-use pipeline for organelle phylogenomics based on homologous blocks searching. ? Instead of genes, locally collinear blocks among organelle genomes are recognized for constructing multi-sequence alignments. ? Non-coding regions, unannotated coding genes and rRNA genes are taken into account for reconstructing the phylogenetic tree. ? HomBlocks will potentially facilitate a better understanding of phylogenic relationships at the organelle genome level.
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