TreeDyn enables graphical analysis according to two directions: localisation or labelisation (Figure 1). Localisation enables the selection of leaves names and then finds out the coresponding graphical elements. Labelisation enables the selection of graphical elements such as subtrees, and then finds out what are the corresponding leaves names. A graphical operation must be selected for highlighting items, such as switching the foreground color to green, update leaves names to a given font and so on.

TreeDyn enables localisation and labelisation operations using information linked to leaves (Figure 2). This information, either quantitative (for instance latitude, longitude, etc.) or qualitative (country names for instance), is organize within a leaves*variables data matrix. Using the "Identification panel" of TreeDyn, the user can load such labels matrix and querying these data for having elaborated localisations or labelisations. For instance, switching the foreground color to green of graphical items (leaves, subtree) linked to leaves of a given country.

Figure 1 User's selection of items from a list and highlighting the corresponding graphical elements is called localisation. User's selection of graphical items and highlighting the corresponding elements from a list is called labelisation. The highlighting operation works on leaves or subtrees, it can operate on graphical variables such as foreground or background colors, font, line (width, dash) or adding symbols, annotations, shrinking/collapsing items and so on.

Figure 2 Identification (Localisation and Labelisation) is powerfull when used in conjonction with information linked to leaves. A species phylogeny can be linked to biosystematic data, geographical or epidemiological information. A classification tree of genes, proteins or DNA array data can be associated to data such as molecular functions, cellular roles, functionnal categories etc.

1. Dowload and open this tree
2. Pop-Up the "Identification Panel": select the "Identification Panel" option from the "View" menu of the main TreeDyn panel
3. Figure 3.1 Dowload and open these annotations (t2.tlf) using the "Load" option from the "File" menu of the "Identification panel"
4. Figure 3.2 Target the tree from the "Target(s)" menu (by default the last open tree is the current target tree)
5. Figure 3.3 Select the "Node Foreground Color" option from the "Operation" menu
6. Figure 3.4 From the "Reset" menu check on the "Automatic reset" option for "Node Foreground Color"

1. Figure 4.1 within the listboxes section of the "Identification panel" built a query by selecting listed items from the "Select", "Variable", "Operator" and "Value" sections, for instance select respectively :
   • "select EU from t2 where"
   • "FuncCat"
   • "##"
   • "ATPase"
2. Figure 4.2 click the "Query" button. The query "select EU from t2 where FuncCat ## ATPase" is showed is the console window section of the "Identification panel". This query means we want to extract the leaves (the EU keyword) whose contain (the ## operator) the "ATPase" keyword for the "FuncCat" variable. We use the "##" operator because the FuncCat variable is multivalued (the "!#" operator means "do not contains" and is also used in case of multivalued variables)
   
   TreeDyn returns a list of matching leaves (green text) for each target(s) tree(s). In this example, there is only one tree, "t2", which have 24 matching leaves. That is to say there is 24 leaves in the tree we are analysing with the keyword "ATPase" as a value for the FuncCat variable in the t2 labels matrix.
3. Figure 4.3 TreeDyn highlight the matching leaves in the tabular view section of the "Identification panel" (the rows with a yellow background color). This is done considering all the leaves listed in the labels file, whitout tree consideration. In our example, there is 200 matching leaves with a "ATPase" value for the "FuncCat" variable (blue text) for a total of 6419 leaves listed in the labels file.
   
   
4. Figure 5 The 24 matching leaves of the "t2" tree are located on the tree knowing the highlighting operation: "Node Foreground Color". Here, if several matching leaves share a common node, the corresponding subtree is highlighted. You can select another color for this operation by using the "Color/Font panel" option from the "View" menu of the TreeDyn main panel.
   
   

   Figure 4

   Figure 5 Locating leaves having a "ATPase" activity Query: select EU from t2 where FuncCat ## ATPase