TreeDyn FAQ
How To ? / FAQ
Table of contents

  1. How to make a label file
  2. How to translate a Leaves*Variables data matrix to a TreeDyn labels file
  3. How to target/untarget one or several tree(s) ?
  4. How to initialize the graphicals variables of tree(s) ?
  5. How to open several trees in a one way process ?
  6. How to import a Nexus files ?
How to make a label file

A labels file is set of records in a text file format. There is one record per row in a label file. A record begin with the name of a leaf which is followed by a list of variable/value(s) pairs.

Ex. 1:
SKI2 Subcellular_loc Cytoplasmic Cellular_Role RNA_turnover FuncCat RNA-binding_protein
SKI3 Subcellular_loc {Cytoplasmic Nuclear} Cellular_Role RNA_turnover

The Ex.1 is a labels file with 2 records. The first row is a record related to the "SKI2" leaf. There is 3 variables : Subcellular_loc, Cellular_Role and FuncCat. Each variable have a value, respectively: Cytoplasmic, RNA_turnover and RNA-binding_protein. The second row is a record related to the "SKI3" leaf. This record has 2 variables which are Subcellular_loc and Cellular_Role. Here, the variable Subcellular_loc is multi-valued : Cytoplasmic and Nuclear. Brackets must be used for such a list of values. Also, the FuncCat variable is not present in the SKI3 record, simply because we do not have information for this leaf regarding this variable.

Nota Bene:
  1. brackets "{" and "}" must be used for list of values.
  2. brackets "{" and "}" must be used with variables names containing spaces.
  3. records of a given labels file do not have necessary the same variables list. In case of unknown values it is nevertheless possible to used generic values such as "0", "Unknown", "NS", and so on
  4. there is no order to respect in the variable/values pair list between the differents records.
  5. leaves names, variable names and values are string characters without space.
  6. leaves names, variables and their values do not contain the following characters: {, }, (, ), [, ], *, ?, ". Numbers are possibles.
  7. for localisation/labelisation processes the leave names must be exactly the same between the graphical representation and the label file. In particular upper/lower cases must be respected.
  8. a given label file may contains several records related to the same leave, with or without new variables.
  9. it is possible to distributed information on differents labels files.
If you have a leaves (rows) * variables (columns) labels matrix, you may translate it into a TreeDyn labels file using the Library panel (option 4).
How to translate a Leaves*Variables data matrix to a TreeDyn labels file

How to target/untarget one or several tree(s) ?

How to initialize the graphicals variables of tree(s) ?

How to open several trees in a one way process

Select the Open option of the File menu from the main TreeDyn panel. Select tree(s) file(s) using the Shitf or Ctrl keys and whatever their formats (Newick and/or TGF). Moreover, one file may contains several newick strings. The selected tree(s) will be opened in one window. Use the "Reorganize" command from the navigation menu of the Canvas contextual menu for organising the trees in rows*columns
How to import a Nexus files ?

Nexus files needs a translation for being readable by TreeDyn. From the main TreeDyn panel, pop-up the Libray panel, activate the tab number 4. Select the Nexus file you want to translate, the name of the new file, then clic the ok button.