Chen Wei-Hua, Lercher Martin J
Bioinformatics, Heinrich-Heine University Duesseldorf, 40225, Germany.
BMC Res Notes. 2009 Jul 31;2:155. doi: 10.1186/1756-0500-2-155.
Genome sequencing projects and comparative genomics studies typically aim to trace the evolutionary history of large gene sets, often requiring human inspection of hundreds of phylogenetic trees. If trees are checked for compatibility with an explicit null hypothesis (e.g., the monophyly of certain groups), this daunting task is greatly facilitated by an appropriate coloring scheme.
In this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation as a stand-alone command line tool, and its application can thus be easily automated. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes.
ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files.
基因组测序项目和比较基因组学研究通常旨在追溯大型基因集的进化历史，这往往需要人工检查数百个系统发育树。如果通过与明确的零假设（例如某些类群的单系性）来检查树的兼容性，那么适当的着色方案将极大地便利这项艰巨的任务。
在本报告中，我们介绍了ColorTree，这是一种用于系统发育树的简单而强大的批量定制工具。基于模式匹配规则，ColorTree对输入的树文件应用一组定制，例如给标签或分支着色。定制后的树被保存到一个输出文件中，然后可以通过Dendroscope（一个免费的树查看器）进行查看和进一步编辑。ColorTree作为一个独立的命令行工具在任何安装了Perl的环境中运行，因此其应用可以很容易地实现自动化。通过这种方式，数百个系统发育树可以在几分钟内被定制以便于直观检查。
通过将用户提供的配置文件应用于多个树文件，ColorTree允许对大型树集进行高效且灵活的可视化定制。
