BACKGROUND Studying site-specific amino acid frequencies by eye can reveal biologically significant variability and lineage-specific adaptation. This so-called 'sequence gazing' often informs bioinformatics and experimental research. But it is important to also account for the underlying phylogeny, since similarities may be due to common descent rather than selection pressure, and because it is important to distinguish between founder effects and convergent evolution. We set out to combine phylogenetic and sequence data to produce evolutionarily insightful visualisations. RESULTS We present ChromaClade, a convenient tool with a graphical user-interface that works in concert with popular tree viewers to produce colour-annotated phylogenies highlighting residues found in each taxon and at each site in a sequence alignment. Colouring branches according to residues found at descendent tips also quickly identifies lineage-specific residues and those internal branches where key substitutions have occurred. We demonstrate applications of ChromaClade to human immunodeficiency virus and influenza A virus datasets, illustrating cases of conservative, adaptive and convergent evolution. CONCLUSIONS We find this to be a powerful approach for visualising site-wise residue distributions and detecting evolutionary patterns, especially in large datasets. ChromaClade is available for Windows, macOS and Unix or Linux; program executables and source code are available at github.com/chrismonit/chroma_clade .

中文翻译：

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ChromaClade：系统发育和序列数据的组合可视化。


背景技术通过肉眼研究位点特异性氨基酸频率可以揭示生物学上显着的变异性和谱系特异性适应性。这种所谓的“序列凝视”通常为生物信息学和实验研究提供信息。但重要的是还要考虑潜在的系统发育，因为相似性可能是由于共同血统而不是选择压力，而且区分创始人效应和趋同进化也很重要。我们着手将系统发育和序列数据结合起来，以产生具有进化洞察力的可视化结果。结果我们推出了 ChromaClade，这是一种带有图形用户界面的便捷工具，可与流行的树查看器配合使用，生成带颜色注释的系统发育图，突出显示每个分类单元和序列比对中每个位点中发现的残基。根据在后代尖端发现的残基对分支进行着色也可以快速识别谱系特异性残基以及发生关键替换的内部分支。我们展示了 ChromaClade 在人类免疫缺陷病毒和甲型流感病毒数据集上的应用，说明了保守进化、适应性进化和趋同进化的案例。结论我们发现这是一种可视化位点残基分布和检测进化模式的强大方法，特别是在大型数据集中。 ChromaClade 适用于 Windows、macOS 和 Unix 或 Linux；程序可执行文件和源代码可在 github.com/chrismonit/chroma_clade 获取。