TreeDyn User's Manual
TreeDyn Tutorial Basic Operations

Abstract

The tutorial is an introduction to TreeDyn, which organize graphical functions into 8 families : Navigation, Figuration, Annotation, Identification, Conformation, Abstraction, Reflection and Illustration. There is 3 more groups called Import/Export, Scripting and Library. The tutorial #01 give examples on how to use several functions from these families, either by using tools represented by icons and are useable "on the fly" to the graphic elements and by using contextual menus linked to graphicals items. Once you have loaded a tree, you can access each step of the tutorial independantly from the others.


Table of contents
Table of contents:

    Import/Export:
  1. Opening a tree
    Navigation:
  2. Moving a tree
  3. Resizing a tree
  4. Zooming in/out a tree
    Figuration:
  5. Modifying a sub-tree foreground color
  6. Modifying a sub-tree background color/stipple
  7. Modifying the foreground color of leaves
  8. Modifying leaves font
  9. Initializing to the default Figuration variables
    Annotation:
  10. Annotating a sub-tree with text
  11. Annotating a sub-tree with symbols
  12. Annotating a set of leaves with text
  13. Annotating a set of leaves with a symbol
  14. Displaying branch lenghts
    Conformation:
  15. Swaping a sub-tree
  16. Outgrouping a sub-tree
  17. Switching between configurations (Rectangular, Circular...)
    Abstraction:
  18. Shrinking a subtree
    Import/Export:
  19. Saving as TGF data
Data:
Data set #1 Newick

Conventions:
  • M1 = Left Mouse Button
  • M3 = Right Mouse Button
  • CM = Contextual Menu with M3

Opening a tree
  • Download and open this tree (Main TreeDyn Panel / File menu / Open command)
  • by default, tree height is calculated for non-recovering leaf labels
  • by default, TreeDyn documents are 300X300 pixels
  • by default, leaves font is {Arial 7 normal}
  • leaf labels may contain white space
  • the tree format is either Newick or TGF (see FAQ for Nexus importation)
  • Newick strings may integrate branch lengths and/or bootstrap values: (a:$bl,b:$bl)$bv:$bl
  • Newick strings may be symbolic (no number, neither branch length or bootstrap values): ((a,b),c)
  • one file may contains several Newick strings
  • you can open several files in one window using the Shift/Ctrl keys (whatever the trees format)

  • Moving a tree
  • use the canvas scrollbars
  • activate the Move tool
  • M1 near the tree and drag it
  • the move tool can be applied on all the canvas items (annotations, symbols...)
  • translation is hierachical : a node annotation can be moved independently from the corresponding subtree, but moving the tree also translated all its annotations
  • Shift-M1 move all the items of a canvas

  • Resizing a tree
  • CM tree (M3 near a tree), Navigation menu, "Resize..."
  • set new width and height values, then clic "Apply"

  • CM tree, Navigation menu, "Fit to window" : resize the tree to the window size
  • CM canvas, Navigation menu, "Resize..." : resize all the trees of the corresponding window
  • "Tree panel" resize all the targeted trees, whatever their window (see FAQ for tree targetting system)

  • Zooming in/out a tree
  • activate the tool
  • M1 near the tree, the tree Zoom In among the x & y axis
  • Shitf-M1 near the tree, the tree Zoom Out among the x & y axis
  • Main TreeDyn Panel activate the tool
  • M1 near the tree (or Shitf-M1), the tree Zoom In (or Zoom Out respectively) among the x axis only
  • Main TreeDyn Panel, activate the tool
  • M1 near the tree (or Shitf-M1), the tree Zoom In (or Zoom Out respectively) among the y axis only

  • Modifying a sub-tree foreground color
  • select the tool
  • Main TreeDyn Panel / View Menu / command "Parameters Panel (Color/Font/Stipple/Symbol/Text)"
  • Parameters Panel / Color tab / select a color
  • M1 on a node
  • Shift-M1 set the subtree foreground color to default one
  • setting a new foreground color to an internal node will erase all the foreground color of the sub-internal nodes.

  • Modifying a sub-tree background color/stipple
  • Main TreeDyn Panel, select the tool
  • Main TreeDyn Panel / View Menu / command "Parameters Panel (Color/Font/Stipple/Symbol/Text)"
  • Parameters Panel / Color tab / select a color
  • Parameters Panel / Stipple tab / select a stipple
  • M1 on a node
  • select another color
  • M1 on a node under the previous one
  • select another color
  • M3 on the first background then select the command "Update color"
  • Shift-M1 remove a sub-tree background
  • setting sub-tree background never delete previous background (neither from root to leaves or leaves to root)
  • TreeDyn manage several background shapes (CM the background)
  • Stipple are transparents

  • Modifying the foreground color of leaves
  • select the tool
  • Main TreeDyn Panel / View Menu / command "Parameters Panel (Color/Font/Stipple/Symbol/Text)"
  • Parameters Panel / Color tab / select a color
  • M1 the node corresponding to the set of leaves you want to foreground color
  • Shift-M1 on a node set the corresponding leaves foreground color to the default one

  • Modifying leaves font
  • activate the tool
  • Main TreeDyn Panel / View Menu / command "Parameters Panel (Color/Font/Stipple/Symbol/Text)"
  • Parameters Panel / Font tab / select a font
  • M1 the node corresponding to the set of leaves you want to modify the font
  • M1 or Shift-M1 on a node to inrease or to decrease respectively the font size
  • M1 switch Italic on/off
  • M1 switch Underline on/off
  • M1 switch Bold on/off
  • M1 switch Overstrike on/off

  • Initializing to the default Figuration variables
  • all the trees of a window: canvas CM / "Reset/Remove" / Select the graphicals variables you want to reset
  • a given tree: tree CM / "Reset/Remove" / Select the corresponding graphical variable you want to reset
  • a given sub-tree: node CM / "Reset/Remove" / Select the corresponding graphical variable you want to reset

  • Annotating a sub-tree with text
  • select the tool
  • Parameters Panel / Text tab / enter text
  • M1 the node corresponding to the sub-tree you want to annotate
  • select the tool
  • M1 the previous annotation and drag it
  • Parameters Panel / Color tab / select the color you want to use for the annotation
  • Parameters Panel / Font tab / select the Font you want to use for the annotation
  • M3 the annotation: update the color, the font or delete the annotation

  • Annotating a sub-tree with symbols
  • select the tool
  • Parameters Panel / Symbol tab / select a symbol
  • M1 the node corresponding to the sub-tree you want to annotate
  • select the tool
  • M1 the previous annotation and drag it
  • Parameters Panel / Color tab / select a new color you want to use for the annotation
  • Parameters Panel / Symbol tab / select a new symbol you want to use for the annotation
  • M3 the annotation: update the color, the symbol or delete the annotation

  • Annotating a set of leaves with text
  • select the tool
  • Parameters Panel / Text tab / enter text
  • M1 the node corresponding to the leaves you want to annotate
  • Parameters Panel / Text tab / select the tool
  • M1 the annotations and drag them (only among the x axis)
  • Parameters Panel / Color tab / select a new color you want to use for the set of annotations
  • Parameters Panel / Font tab / select a new font you want to use for the annotations
  • M3 the annotation: update the color or the font
  • M3 the annotation: you can delete one annotation, a given set or all the leaves annotations
  • Parameters Panel / Text tab / : respectively new color by column or by row, new font by column or by row and text anchoring (west or east)
  • Parameters Panel / Text tab / for moving all the leaves annotations (only x axis)
  • Parameters Panel / Text tab / If the "Tabulation" checkbox is "on", annotations sets will be tabulated automatically. You can use the "preview" button for knowing where annotations will be inserted. Use the "+" and "-" buttons for manual tabulations.

  • Annotating a set of leaves with a symbol
  • select the tool
  • Parameters Panel / Symbol tab / select a symbol
  • M1 the node corresponding to the leaves you want to annotate
  • Parameters Panel / Symbol tab / select the tool
  • M1 the annotatation set and drag it (only among the x axis)
  • Parameters Panel / Color tab / select a new color you want to use for the set of annotations
  • M3 the annotation: update the color of the symbol
  • M3 the annotation: you can delete one annotation, a given set or all the leaves annotations
  • Parameters Panel / Symbol tab / : respectively new color by column or by row
  • Parameters Panel / Symbol tab / for moving all the leaves annotations (only x axis)
  • Parameters Panel / Symbol tab / If the "Tabulation" checkbox is "on", annotations sets will be tabulated automatically. You can use the "preview" button for knowing where annotations will be inserted. Use the "+" and "-" buttons for manual tabulations.

  • Displaying branch lenghts
  • CM Tree / "Display Newick Annotations"
  • select
  • M1 the node corresponding to the branch length you want to insert
  • Shift-M1 in percent
  • extract and post information from after the ":" character of the corresponding node
  • extract and post information from before the ":" character of the corresponding node
  • information from before or after the ":" character may be qualitative

  • Swaping a sub-tree
  • Select the tool
  • M1 the node corresponding to the subtree you want to swap

  • Outgrouping a sub-tree
  • Select the tool
  • M1 the node corresponding to the subtree you want to outgroup
  • The outgroup operation will destroy all the figuration variables (color, font, etc.) and the annotations

  • Switching between configurations (Rectangular, Circular...)
  • CM Tree, Conformation menu
  • Select a tree configuration, for instance "Circular with branch length"
  • Figuration and Annotation variables will not be deleted by the configuration switch

  • Shrinking a subtree
  • Select the tool
  • M1 the node corresponding to the subtree you want to shrink
  • M1 the shrink symbol to unshrink the subtree
  • CM the shrink symbol for having information related to the corresponding subtree
  • shrinking a node keep the space of the corresponding subtree
  • shrinking a subtree keep all its graphical variables

  • Saving as TGF data
  • Main TreeDyn Panel / File menu
  • select the "Save..." menu
  • select the corresponding TreeDyn document and save the graphic
  • Main TreeDyn Panel / File menu
  • select the "Open..." option and open the previous saved document
  • the graphic is saved under the TGF format (TreeDyn Graphic File)
  • TGF save all the features of TreeDyn documents and you can restore them later