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MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

Chen SC, Ogata A - PLoS ONE (2015)

Bottom Line: 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.The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics, Idaho State University, Pocatello, Idaho, United States of America.

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.

No MeSH data available.


Related in: MedlinePlus

An Example of Distances Support in the Viewer.
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pone.0118893.g008: An Example of Distances Support in the Viewer.

Mentions: The branch lengths (either internal or external) represent the distance information for the time that merged the two sequences. The distance information is written in the Newick file generated by MixtureTree or other packages. The display of distance could be edited by the function panel in FigTree by clicking the following: 'Branch Labels' >'Branch lengths (raw)' in' Display'; a pull-down menu is shown in Fig 8.


MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

Chen SC, Ogata A - PLoS ONE (2015)

An Example of Distances Support in the Viewer.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4380466&req=5

pone.0118893.g008: An Example of Distances Support in the Viewer.
Mentions: The branch lengths (either internal or external) represent the distance information for the time that merged the two sequences. The distance information is written in the Newick file generated by MixtureTree or other packages. The display of distance could be edited by the function panel in FigTree by clicking the following: 'Branch Labels' >'Branch lengths (raw)' in' Display'; a pull-down menu is shown in Fig 8.

Bottom Line: 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.The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics, Idaho State University, Pocatello, Idaho, United States of America.

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.

No MeSH data available.


Related in: MedlinePlus