Galisteo Cristina, de la Haba Rafael R
Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012, Sevilla, Spain.
Department of Animal Health, Faculty of Veterinary, University of León, 24007, León, Spain.
BMC Bioinformatics. 2025 Jun 5;26(1):154. doi: 10.1186/s12859-025-06178-1.
Phylogenetic trees are essential diagrams used in different sciences, such as evolutionary biology or taxonomy, and they depict the relationships between a given set of taxa sharing a common ancestor. So far, a multitude of tools have already been developed to infer phylogeny, and even more to visualize the resulting trees. However, editing generated graphical plots to obtain ready-to-publish figures is still a major issue. Most available tools do not take into consideration important aspects in nomenclature, such as the use of italics for taxon names or the superscript that must be displayed after the strain/specimen designation to denote the type strain/specimen, at least not automatically. A gap also exists to easily highlight tree branches conserved across different phylogenies containing the same taxa. The lack of available tools to achieve these tasks is challenging for scientists, since manual formatting of phylogenetic trees is very time-consuming.
Here, we present a tool named 'gitana', running in Linux/Windows/Mac operating systems with R software installed. It creates ready-to-publish trees with formatting taxon nomenclature and editing options such as rerooting, clade highlighting or collapsing, among other features. Moreover, 'gitana' performs node comparisons among phylogenies comprising the same taxa to identify conserved branches.
'gitana' is a user-friendly tool to output high-quality and ready-to-publish phylogenetic trees for users without R-coding skills. It combines dedicated functions of popular R packages for phylogeny and graphical visualization into an easy one-line-command. The users' manual and source code are freely available at https://github.com/cristinagalisteo/gitana .
系统发育树是不同学科（如进化生物学或分类学）中使用的重要图表，它们描绘了共享共同祖先的一组给定分类单元之间的关系。到目前为止，已经开发了大量工具来推断系统发育，甚至更多工具用于可视化生成的树。然而，编辑生成的图形以获得可直接发表的图表仍然是一个主要问题。大多数现有工具没有考虑命名法中的重要方面，例如分类单元名称使用斜体，或者在菌株/标本指定后必须显示的上标以表示模式菌株/标本，至少不会自动考虑这些。在轻松突出显示包含相同分类单元的不同系统发育中保守的树枝方面也存在差距。由于系统发育树的手动格式化非常耗时，缺乏实现这些任务的可用工具对科学家来说具有挑战性。
在这里，我们展示了一个名为“gitana”的工具，它可以在安装了R软件的Linux/Windows/Mac操作系统上运行。它可以创建具有格式化分类单元命名法和编辑选项（如重新生根、分支突出显示或折叠等）的可直接发表的树。此外，“gitana”在包含相同分类单元的系统发育之间进行节点比较，以识别保守的树枝。
“gitana”是一个用户友好的工具，可为没有R编码技能的用户输出高质量且可直接发表的系统发育树。它将用于系统发育和图形可视化的流行R包的专用功能组合成一个简单的单行命令。用户手册和源代码可在https://github.com/cristinagalisteo/gitana上免费获取。
