Abstract
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.
Highlights
The Newick tree format [1] is used in many scientific disciplines, with a major role in reconstructive phylogeny
MEGA [3], Mesquite [6], PHY-FI [7], TreeView [8], and Geneious [9], the most popular programs that allow the user to add color to a Newick tree, require the user to manually add color to each node; this can result in repetitive clicking with a high potential for human error
TreeGraph [10] allows the user to automatically color a tree to some extent, but it can only color based on a number, such as branch length
Summary
The Newick tree format [1] is used in many scientific disciplines, with a major role in reconstructive phylogeny. The MixtureTree Annotator allows the user to automatically color any given Newick tree generated by many popular software packages, including but not limited to MixtureTree [2], MEGA [3], MrBayes [4], and SeaView. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides an advantage over other current programs. MEGA [3], Mesquite [6], PHY-FI [7], TreeView [8], and Geneious [9], the most popular programs that allow the user to add color to a Newick tree, require the user to manually add color to each node; this can result in repetitive clicking with a high potential for human error. A program that provides similar coloring abilities to MixtureTree Annotator is ColorTree [12], but it does not provide annotation abilities
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