As different taxa evolve, gene order often changes slowly enough that chromosomal ‘blocks’ with conserved gene orders (synteny) are discernible. The MCScanX toolkit (https://github.com/wyp1125/MCScanX) was published in 2012 as freely available software for the detection of such ‘colinear blocks’ and subsequent synteny and evolutionary analyses based on genome-wide gene location and protein sequence information. Owing to its simplicity and high efficiency for colinear block detection, MCScanX provides a powerful tool for conducting diverse synteny and evolutionary analyses. Moreover, the detection of colinear blocks has been embraced as an integral step for pangenome graph construction. Here, new application trends of MCScanX are explored, striving to better connect this increasingly used tool to other tools and accelerate insight generation from exponentially growing sequence data. We provide a detailed protocol that covers how to install MCScanX on diverse platforms, tune parameters, prepare input files from data from the National Center for Biotechnology Information, run MCScanX and its visualization and evolutionary analysis tools, and connect MCScanX with external tools, including MCScanX-transposed, Circos and SynVisio. This protocol is easily implemented by users with minimal computational background and is adaptable to new data of interest to them. The data and utility programs for this protocol can be obtained from http://bdx-consulting.com/mcscanx-protocol.

随着不同分类群的进化，基因顺序通常变化得足够慢，以至于具有保守基因顺序（同线性）的染色体“块”是可辨别的。MCScanX 工具包 (https://github.com/wyp1125/MCScanX) 于 2012 年作为免费软件发布，用于检测此类“共线块”以及基于全基因组基因位置和蛋白质序列信息的后续同线性和进化分析。由于共线块检测的简单性和高效率，MCScanX 为进行不同的同线性和进化分析提供了强大的工具。此外，共线块的检测已被视为泛基因组图构建的一个不可或缺的步骤。在这里，我们探讨了 MCScanX 的新应用趋势，力求更好地将这一日益使用的工具与其他工具连接起来，并加速从指数级增长的序列数据中生成洞察。我们提供详细的协议，涵盖如何在不同平台上安装 MCScanX、调整参数、根据国家生物技术信息中心的数据准备输入文件、运行 MCScanX 及其可视化和进化分析工具，以及将 MCScanX 与外部工具（包括 MCScanX）连接-转置、Circos 和 SynVisio。该协议可由具有最少计算背景的用户轻松实现，并且适用于他们感兴趣的新数据。该协议的数据和实用程序可以从 http://bdx-consulting.com/mcscanx-protocol 获取。