TreeDyn User's Manual
TreeDyn Tutorial Reflection - Multi-trees graphical analysis
Abstract

The tutorial is related to trees collections graphical management, from basic operations, like resizing a set of trees, to more complex operations, like Identification and Reflection. The tutorial is based on a data set used in (Simon et al., 2005)(1).



(1) Physical and Partial Genetic Map of Spodoptera frugiperda Nucleopolyhedrovirus (SfMNPV) Genome
Simon O, Chevenet F, Williams T, Caballero P, Lopez-Ferber M
Virus Genes, Vol. 30, No. 3. (2005), pp. 403-417 ( Full pdf document)

Table of contents
Table of contents:

Basic operations Comparative analysis: Identification Comparative analysis: Reflection Data:
Data set #1 Newick TGF Annotations
Data set #2 Newick TGF Annotations

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

  • "Open tree(s)..." control from the File (main TreeDyn panel). Select tree(s) file(s) using the Shitf or Ctrl keys.
  • Open a file containing multiple newick strings
  • TreeDyn Document's contextual menu, and use the "Add tree(s)..." control
  • Copy/Paste processes

    • Resizing and matrix organization of trees

    1. open a raw collection of trees (for instance, http://www.treedyn.org/manual/data/t3a.nwk)
    2. pop-up the "Tree panel" (menu "View" from the main TreeDyn panel)
    3. set tree height to 200 and tree width to 50, click the "Ok" button. All the trees of the collection have now the specified size
    4. "Tree panel": set the number of columns to 7, click the "Ok" button. The collection of trees is now organised in a 7x4 matrix of trees.
    5. Move one tree by using M1 with
    6. Move the entire collection by using Shift-M1 with
    7. Save the collection under the TGF format (Main treeDyn panel, File menu, Save option), let's say we save it under the name tc.tgf
    8. Exit and re-launch TreeDyn, open the tc.tgf file. The TGF format keeps the size and the matrix organization of the trees collection
    9. the rowsXcolumns organisation takes into account tree annotations for allocation of space between trees

    Zooming In/Out a set of trees

    1. open a collection of trees (for instance, http://www.treedyn.org/manual/data/t3a.tgf)
    2. select the tool
    3. M1 the document displaying the trees collection and drag the mouse. All the trees are zoom in/out, following the mouse mouvement, here the width/height ratio is locked
    4. select the tool
    5. M1 the document displaying the trees collection and drag the mouse. All the trees are zoom in/out, but the width/height ratio is free
    6. the tools & zoom in/out with a locked height or a locked width respectively
    7. a single tree is zoomable independently of the others by using the tools

    Others basic operations: font, conformation...

    1. open a collection of trees (the collection saved previously or http://www.treedyn.org/manual/data/t3a.tgf)
    2. pop-up the "Parameters panel (Color/Font/Stipple/Symbol/Text)" (menu "View" from the main TreeDyn panel), click the "Font" tab, modify the current font (for instance set the "Family" variable to "Small Fonts" and the "Size" variable to the value "6")
    3. M3 the TreeDyn document (be sure to have the document contextual menu by M3 away from a tree, check the title of the contextual menu) and select the "Update Leaves Font" option. All the leaf labels font is set to the current font.
    4. M3 the TreeDyn document (be sure to have the document contextual menu by M3 away from a tree, check the title of the contextual menu) and select the "Conformation" sub-menu, and finally the "Circular (Internal)" conformation. All the trees are set to the selected configuration. Click the "Ok" button for rowsXcolumns organisation ("Tree panel") for a matrix refresh view. the "Tree panel"
    5. Do it again, but this time, select the rectangular conformation (with branch length). As you see switching between different conformation have an impact to the size of tree. Click the "ok" buttons from the "Tree panel", first for size, then for rowsXcolumns.

    Pattern matching on leaf labels ("Find panel")

  • see the Identification - Querying leaf labels Tutorial
  • The "Find" operator works on multiple trees, whatever their window(s)

    • Multi-Localization ("Identification panel")

  • see the Identification - Locating & Labelling Tutorial
  • The Identification operator works on multiple trees, whatever their window(s)

    • Reflection with a same leaf labels set between trees

    1. download and open http://www.treedyn.org/manual/data/t3a.nwk There is 27 trees/27 genes for 19 amino-acids sequences/19 virus species. The leaf labels have been translated from the ORFs sequences to to species names. So the differents genes phylogenies are now based on the same leaf labels set. "Cuni" is the outgroup.
    2. organize the trees collection: for instance tree size 50x200 and tree matrix 10x3
    3. select the "Transition" tool: , a "Operation" menu pop-up. The default operation is "Leaf Foreground Coloré
    4. "Operation" menu: select "Node Foreground Color"
    5. pop-up the TreeDyn "Parameters panel (Color/...)" and select a color (let's say blue)
    6. apply the Transition tool on a subtree: its foreground color is updated to blue, and the Transition operator also highlights every corresponding leaf label on others trees and potentialy sub-trees, depending of their topologies and knowing that we are using a Node graphical operation.
    7. "Operation" menu: select "Leaf Background Color", select a green color, and M1 a subtree
    8. from the main TreeDyn panel, select the "Reset" tool , M1 the trees document, and select the control "Leaves: Background color".
    9. NB: the Transition operator works on the targeted trees, whatever their window. From a given source tree, you can target several trees from differents TreeDyn documents. Target/Untarget trees by using the "Tree panel"

    Reflection with differents leaf labels sets between trees

  • download and open http://www.treedyn.org/manual/data/t3b.nwk This is the same dataset as the pevious one but here the trees use original ORF names as leaf labels. Moreover, a consensus tree has been added (based on species names)
  • Trees organisation... 50x200, 10x3
  • download the following annotations file: http://www.treedyn.org/manual/data/t3b.tlf
  • load the annotations file (main TreeDyn panel, File menu, "Load annotations...")
  • select the following "Transition" tool: , a "Operation" menu pop-up.
  • M1 a subtree from the CONSENSUS tree, and select the "Transition" variable.
  • if you have a look to the annotations file, the previous operation is based on the following records :
    ACM Transition {Ac002 Ac002 Ac002 Ac002 Ac006 Ac008 A... }
    ADO Transition {Ado001 Ado002 Ado003 Ado006 A...}
    BM Transition {Bm001 Bm002 Bm003 Bm005 Bm006 Bm007 Bm009 ...}
    CP Transition {Cp001 Cp002 Cp003 Cp007 Cp008 Cp009 ... }
    CUNI Transition {Cun008 Cun014 Cun018 Cun023 Cun024 ... }
    ...

    when you select a subtree (from the consensus tree), you select a set of leaf labels, for instance ADO, PHOP and CP. For each of these labels, the Reflection operator query the "Transition" variable (the one you choose). For instance the value of the Transition variable for the ADO entry is "Ado001 Ado002 Ado003 Ado006...". In the context of the Reflection operator, this means that if you highlight the ADO leaf label, you also highlight the "Ado001 Ado002 Ado003 Ado006..." leaf labels.
  • but how highlighting beetween ORF trees ? Select the following "Transition" tool:
  • M1 a subtree from another tree than the consensus one, and select the Transition variable.
  • if you have a look to the annotations file, you will find the following records :
    Cp001 Transition CP
    Cp002 Transition CP
    Cp003 Transition CP
    ...
    Phop001 Transition PHOP
    Phop002 Transition PHOP
    Phop003 Transition PHOP
    ...
    Ado001 Transition ADO
    Ado002 Transition ADO
    Ado003 Transition ADO
    ...

    when you select a subtree, you select a set of leaf labels, for instance Cp002 Phop002 and Ac002. For each of these labels, the Reflection operator query the "Transition" variable (the one you choose). For instance the value of the Transition variable for the Cp002 entry is "CP". In the context of the Reflection operator, this means that if you select the Cp002 leaf label, you also select all the leaf labels having the same value for the Transition variable, that is to say, all the leaf labels having the CP value for Transition
  • note that this operator is functionnal with any kind of variable (a country, a number,...)

  • One annotations file can be used in differents ways according to the Reflection operator or