Department of Computer Science, Auckland University.
Bioinformatics. 2010 May 15;26(10):1372-3. doi: 10.1093/bioinformatics/btq110. Epub 2010 Mar 12.
Bayesian analysis through programs like BEAST (Drummond and Rumbaut, 2007) and MrBayes (Huelsenbeck et al., 2001) provides a powerful method for reconstruction of evolutionary relationships. One of the benefits of Bayesian methods is that well-founded estimates of uncertainty in models can be made available. So, for example, not only the mean time of a most recent common ancestor (tMRCA) is estimated, but also the spread. This distribution over model space is represented by a set of trees, which can be rather large and difficult to interpret. DensiTree is a tool that helps navigating these sets of trees.
The main idea behind DensiTree is to draw all trees in the set transparently. As a result, areas where a lot of the trees agree in topology and branch lengths show up as highly colored areas, while areas with little agreement show up as webs. This makes it possible to quickly get an impression of properties of the tree set such as well-supported clades, distribution of tMRCA and areas of topological uncertainty. Thus, DensiTree provides a quick method for qualitative analysis of tree sets.
DensiTree is freely available from http://compevol.auckland.ac.nz/software/DensiTree/. The program is licensed under GPL and source code is available.
通过像 BEAST（Drummond 和 Rumbaut，2007）和 MrBayes（Huelsenbeck 等人，2001）这样的程序进行贝叶斯分析，为重建进化关系提供了一种强大的方法。贝叶斯方法的好处之一是可以对模型中的不确定性进行有根据的估计。因此，例如，不仅可以估计最近共同祖先（tMRCA）的平均值，还可以估计其分布。该模型空间中的分布由一组树表示，这些树可能非常大且难以解释。DensiTree 是一种帮助浏览这些树集的工具。
DensiTree 的主要思想是透明地绘制集合中的所有树。因此，拓扑和分支长度上有很多树一致的区域显示为高度着色区域，而一致性较小的区域则显示为网状。这使得快速了解树集的属性成为可能，例如支持良好的进化枝、tMRCA 的分布和拓扑不确定性的区域。因此，DensiTree 提供了一种快速定性分析树集的方法。
DensiTree 可从 http://compevol.auckland.ac.nz/software/DensiTree/ 免费获得。该程序根据 GPL 获得许可，并且可以获得源代码。
