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How to use T-REX
(Macintosh version)

Current release: 1.2a4

What's new

New! Print results directly from the program
New! Progress bars indicate calculations' progress Graphical tree and reticulogram representations
Weighted tree and reticulogram reconstruction methods available
Choose the root of a tree or reticulogram
Choose the color of the drawn reticulations

Using T-REX is easy!

  1. Start the program by double-clicking on its icon Note that there is balloon help in each menu and dialog of the program. You can turn it on and off with the "Help" menu, or click on the lightbulb icon in the T-REX dialog.
  2. Open or Import a dissimilarity matrix
    T-REX requires its input to be in the SIMIL format, used by the R Package. This is a binary format that cannot be created directly in a text editor. These files are created with programs such as Simil and Import-Export of the R Package.
    • If your input file is a text (ASCII) file, then you must import it using the menu command "File...Import". In the resulting dialog, specify what your input file looks like and click "Import". A new window will open containing your imported input file, which may then be used by T-REX to perform tree reconstruction. You can also save the new window in a SIMIL-type file, and open it later.
    • If you already have a SIMIL-type file, then open it using the menu command "File...Open".
    Note that you can't import a rectangular file, since T-REX has no use for them (see below)
  3. Look at the resulting window to ensure that this is the matrix you wanted
  4. Select Reconstruct a tree... or Reconstruct a reticulogram... in the T-REX menu
  5. Choose one of the five tree reconstruction methods for your additive tree (left-hand side of the dialog), and select what to output on the right-hand side.

    If you have chosen to reconstruct a reticulogram, you must select a stopping rule for adding reticulations:

    • When function Q1 reaches its minimum
    • When function Q2 reaches its minimum
    • When K reticulations have been added, where K varies from 0 to (2n-2)(2n-3)/2 - (2n-3).
    For more information about these functions, either turn on Balloon Help in the program, see the User's guide (in .pdf format) included in the distribution or refer to Makarenkov & Legendre (1999).
T-REX will now compute the fitted distance matrix, tree/reticulogram edges and tree/reticulogram statistics which will appear in two windows. One is a SIMIL-type window (same as your input file) which can be saved to disk or exported as text (for use in other programs). You can also select within the window and copy the information to the clipboard, for instance to paste it in a spreadsheet program. The other window is a text display widow which can also be saved, copied to the clipboard and printed (pending implementation in the R Package 4.0. See the Frequently Asked Questions below). If requested, T-REX will also display a graphical representation of the fitted distance matrix (and tree/reticulogram edges) in a separate, resizable window. Three types of graphical representation - hierarchical, radial and axial drawings - are available. The user may also choose the root of the tree over the set of all existing vertices, as well as handle some extra features of the graphical representation. Note: You can modify a window's properties (for instance, header information or drawing characteristics) by selecting Properties in the Edit menu, or by double-clicking in the window. This is especially useful for the tree/reticulogram window.

Frequently Asked Questions

Why must I "Import" my data matrices to use T-REX?

T-REX shares almost all of its user interface routines with the R Package 4.0 being developed by Philippe Casgrain. Therefore, as R 4.0's interface code becomes more robust, T-REX will automatically benefit from the enhancements. Moreover, within R 4.0, there are two data file formats: rectangular (nxp) and SIMIL. Rectangular matrices may have any number of rows (objects) and columns (descriptors, or variables) and contain very different information, from X-Y coordinates to water pH. In contrast, a SIMIL matrix is quite homogeneous, describing only the resemblance between n objects. This type of matrix is thus treated as a special case of the rectangular matrix, and has its own window type: it is symmetrical, the row and column headers are the same, and the diagonal contains either 1s or 0s (if it's a similarity or distance matrix). We felt that since T-REX dealt with dissimilarity matrices, it was much easier to use the routines we had already built and tested for parsing and representing input files rather than reading ASCII text each time. Of course, you can export a SIMIL file to a text file, and you can select and copy from the window with ease (see the "Edit" menu).

Do you plan to add more tree reconstruction methods to T-REX?

Yes! As time allows, we will incorporate new tree reconstruction algorithms to T-REX.

Who do we contact if we have a problem/comment/suggestion... ?

You may contact either Vladimir Makarenkov or Philippe Casgrain.

Last updated on Sunday, August 01, 2010 by Philippe Casgrain
Created on Wednesday, June 10, 1998