Chen Shu-Chuan, Ogata Aaron
Department of Mathematics, Idaho State University, Pocatello, Idaho, United States of America.
School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, Arizona, United States of America; School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona, United States of America.
PLoS One. 2015 Mar 31;10(3):e0118893. doi: 10.1371/journal.pone.0118893. eCollection 2015.
The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.
MixtureTree注释器用Java编写，可让用户自动为从任何系统发育重建程序生成的Newick格式的系统发育树上色，并输出Nexus文件。通过提供按序列名称自动为树上色的功能，MixtureTree注释器相对于执行类似功能的任何其他程序具有独特优势。此外，MixtureTree注释器是唯一能够用突变信息和合并时间信息有效注释MixtureTree产生的输出的软件包。为了可视化生成的输出文件，使用了FigTree的修改版本。某些缺乏良好内置可视化工具的流行方法，例如MEGA、Mesquite、PHY-FI、TreeView、treeGraph和Geneious，可能会由于手动为每个节点添加颜色或存在其他限制（例如仅根据数字（如分支长度）或分类法使用颜色）而产生人为错误的结果。除了允许用户按序列名称自动为任何给定的Newick树上色外，MixtureTree注释器是唯一允许用户自动注释由MixtureTree程序创建的结果树的方法。MixtureTree注释器快速且易于使用，同时仍允许用户完全控制上色和注释过程。
