Bayesian Phylogenetic Diagnostics

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TreeScaper

TreeScaper is a cross-platform software package for calculating and displaying the relationship of tree-to-tree distances in 2d or 3d. With TreeScaper you can:

  • Display 2- or 3d plots of tree-to-tree distances
  • Rotate 3d plots
  • Create movies of rotating 3d plots
  • Color-code set of trees
  • Change the optimization algorithm and cost function used to project tree-to-tree distances in n-dimensions
  • Calculate several goodness of fit measures for your projections of tree-to-tree distances
  • Input tree-to-tree distance matrices output by PAUP*
  • Calculate several intrinsic dimensionality measures for a tree-to-tree distance matrix

Presentation related to TreeScaper

  • Click here to view a poster presented on the subject at the Evolution meeting, Portland, OR, June 25, 2010.
  • Click here to view a talk presented at the iEvoBio meeting, Portland, OR, June 28, 2010.
  • Click here to view a poster presented at the Evolution meeting, Norman, OK, June 19, 2011.

Screen Shots andĀ Image Gallery

TreeScaper has several windows in which options related to the underlying projection method can be changed. In addition, windows are available to change display parameters and to calculate goodness of fit statistics. The main TreeScaper window and a couple example images generated by TreeScaper are displayed below.

Screen shot of the TreeScaper main application window Image of Salamander mtDNA trees with convex hull enclosing gene trees A 3D Image of Tree-to-Tree distances

Software Downloads

Software is being distributed as an Alpha test release. We encourage you to download and try the software and welcome your feedback.

Please send questions, comment, and bug reports to This e-mail address is being protected from spambots. You need JavaScript enabled to view it .

Plotting options

TreeScaper generates 2d and 3d plots with the program by clicking the "Plot" button. Using your mouse you can rotate the 3d plots, zoom in on parts of the graph, and change the plot perspective. In addition, TreeScaper outputs 2d and 3d coordinate files, so that you can use third party plotting packages like Matlibplot to create publication quality figures in a number of output formats. Below are example figures and the Python scripts that were used to generate them. Note, all of these figures were generated using Python and Matlibplot.

image creating using plot maker_2D.py script
Plotmaker_2D.py

image creating using landscape_2Dby4plot.py script
landscape_2Dby4plot.py

Authors

Wen Huang, Jim Wilgenbusch, Kyle Gallivan

 

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