PDF(Pubmed)
Abstract：
Phylogenetic trees illustrate evolutionary relationships between taxa or genes. Tree figures are crucial when presenting results and data, and by creating clear and effective plots, researchers can describe many kinds of evolutionary patterns. However, producing tree plots can be a time-consuming task, especially as multiple different programs are often needed to adjust and illustrate all data associated with a tree. We present TreeViewer, a new software to draw phylogenetic trees. TreeViewer is flexible, modular, and user-friendly. Plots are produced as the result of a user-defined pipeline, which can be finely customised and easily applied to different trees. Every feature of the program is documented and easily accessible, either in the online manual or within the program\'s interface. We show how TreeViewer can be used to produce publication-ready figures, saving time by not requiring additional graphical post-processing tools. TreeViewer is freely available for Windows, macOS, and Linux operating systems and distributed under an AGPLv3 licence from https://treeviewer.org. It has a graphical user interface (GUI), as well as a command-line interface, which is useful to work with very large trees and for automated pipelines. A detailed user manual with examples and tutorials is also available. TreeViewer is mainly aimed at users wishing to produce highly customised, publication-quality tree figures using a single GUI software tool. Compared to other GUI tools, TreeViewer offers a richer feature set and a finer degree of customisation. Compared to command-line-based tools and software libraries, TreeViewer\'s graphical interface is more accessible. The flexibility of TreeViewer\'s approach to phylogenetic tree plotting enables the program to produce a wide variety of publication-ready figures. Users are encouraged to create their own custom modules to expand the functionalities of the program. This sets the scene for an ever-expanding and ever-adapting software framework that can easily adjust to respond to new challenges.
摘要：
系统发育树说明了分类群或基因之间的进化关系。树形数字在呈现结果和数据时至关重要，通过创建清晰有效的地块，研究人员可以描述多种进化模式。然而,生成树图可能是一项耗时的任务，特别是因为经常需要多个不同的程序来调整和说明与树相关的所有数据。我们介绍TreeViewer，绘制系统发育树的新软件。TreeViewer是灵活的，模块化，和用户友好。绘图是作为用户定义的管道的结果而产生的，这可以很好地定制和容易地适用于不同的树木。该程序的每个功能都被记录并易于访问，在在线手册或程序界面中。我们展示了如何使用TreeViewer来生成可用于发布的数字，节省时间，不需要额外的图形后处理工具。TreeViewer可免费用于Windows，macOS,和Linux操作系统，并根据https://treeviewer.org的AGPLv3许可证分发。它有一个图形用户界面（GUI），以及命令行界面，这对于处理非常大的树木和自动化管道很有用。还提供详细的用户手册以及示例和教程。TreeViewer主要针对希望生产高度定制的用户，使用单个GUI软件工具的出版物质量树图。与其他GUI工具相比，TreeViewer提供了更丰富的功能集和更精细的自定义程度。与基于命令行的工具和软件库相比，TreeViewer的图形界面更易于访问。TreeViewer的系统发育树绘图方法的灵活性使该程序能够产生各种各样的出版就绪的数字。鼓励用户创建自己的自定义模块来扩展程序的功能。这为不断扩展和不断适应的软件框架奠定了基础，该框架可以轻松调整以应对新的挑战。
