Add a new tree to a new project

• at the "login" page, click "Use without an account";
• at the "app" page, click the folder icon on the "Basic" tab (the only icon that's clickable if no tree is active). in the popup window, enter the following contents and click the button "Submit" at the bottom:

  
  Project: new project
  
  Name: test tree
  
  Data: (chicken,((mouse,rat),(chimp,human)));
  

• the tree will be shown as the following if there is no error in your input

Change the branch and leaf colors of the tree

in the following we'll add several datasets to change the appearances of the tree.

Let's use the same tree again:

(chicken,((mouse,rat),(chimp,human)));

• First of all add a dataset named "branch colors" to change the colors of the branches by clicking the "branch colors" icon on the "Annotation upload" tab:

• 
  
  
  ## lines start with # are annotations; you can put an annotation line
  ##   anywhere in this dataset, provided that the # is the first character
  ##   of the line
  ## let the dataset begin: all fields of a line are seperated by 'tab'
  ## first all, color all branches with 'grey'
  human,chicken   grey    ad
  ## and then highlight the branches connecting human and chimp
  human,chimp     red     ad
  

  before applying the dataset	http://evdocs.medgenius.info/pictures/Add%20a%20new%20tree%20to%20a%20new%20project.png
  after	http://evdocs.medgenius.info/pictures/branch_color_added_quick_start.png

• then add another dataset to change colors of the tree leaves to match the colors of their corresponding branches by clicking the "tree leaf colors" icon on the "Annotation upload" tab:

• 
      
  
  
  
  
  ## let the dataset begin
  ##   each line of the 'data part' consists three fields sparated by a 'tab' character
  ##   the first field specifies the location on the tree; for example 'human' indicates
  ##     the leaf node representing 'human' or the branch connecting to this leaf node,
  ##     while 'human,mouse' indicates the internal node representing the
  ##     last common ancester (LCA) of human and mouse
  ##   the second field specifies the color to be applied to the corresponding nodes / branches
  ##   the third field is optional; it can be one the following 'key-words':
  ##     ad: the color will be applied to all decendents of the node specified by the first field
  ##     prefix: the color will be applied to all leaf nodes (or connecting branches) whose names
  ##       start with the string in the first field
  ##     suffix: the color will be applied to all leaf nodes (or connecting branches) whose names
  ##       end with the string in the first field
  ##     anywhere: the color will be applied to all leaf nodes (or connecting branches) whose names
  ##       contain the string in the first field
  ## first all, color all leaves to 'grey'
  human,chicken   grey    ad
  ## then, highlight human and chimp with 'red'
  human,chimp     red     ad
  

  after applying the dataset

  http://evdocs.medgenius.info/pictures/leaf_color_quick_start.png

Add pie charts to the tree

From this section we'll add some more complicated datasets to the tree.

First of all, some pie charts; the pies will be displayed on the tree branches.

• click the "piechart" icon on the "Annotation upload" tab:
• copy and paste the following to the text box of the popup dialog box:

• 
  
  
  ## created at may 25, 2011
  ## before the 'data section', now we have a new section that contains
  ##   lines starting with '!'; this section is called the 'modifier section' because
  ##   it's used to change / modify the default behaviors of the dataset
  !Groups A,B,C,D
  !colors #9F0251,#f88ef9,#effc00,#4D8963
  !legendstyle    rect
  !title  example pie chart
  !maxradius      20
  !minradius      8
  !opacity        0.8
  chicken,human   50,0,0,5
  mouse,human     10,0,0,25
  chimp,human     0,20,20,5
  

  and now we have pie charts displayed on the tree branches

  http://evdocs.medgenius.info/pictures/piechart_quick_start.png

Add bar plots to the tree (next to the leaf labels)

Here we'll add some bar plots to the tree; the bars will be plotted next to the leaf labels.

• first of all, click the "bar plots" icon on the "Annotation upload" tab:
• http://evdocs.medgenius.info/pictures/toolbar_barplot_button.png
• choose a name for the dataset and copy and paste the following to the text area in the popup dialog box:

• 
  
  
  ##barplots
  !groups a,b,c
  !colors darkblue,darkgreen,darkred
  !showLegends    0
  !plotwidth      100
  !align
  !grid
  chicken 2,3,1
  mouse   8,9,2
  human   20,3,4
  chimp   10,20,1
  rat     4,6,5
  

  here is how the bars look like

  http://evdocs.medgenius.info/pictures/barplot_quick_start.png

Add colored objects/ shapes to the tree (next to the leaf labels)

Here we'll add a dataset called "color strips / colored shapes".

• click the "color strips" icon on the "Annotation upload" tab:
• http://evdocs.medgenius.info/pictures/toolbar_colorstrips_shapes.png
• copy and paste the following to the text area in the popup dialog box:

• 
  
  
  ##color strips
  !groups a,b,c,d
  !colors blue,green,grey,red
  !type   rect,circle,star,strip
  !showlegends    1
  human   red,green,blue,purple
  chimp   purple,darkred,lightgreen,lightblue
  mouse   lightblue,yellow
  chicken darkgreen,grey,pink,grey
  rat     grey,orange,pink,orange
  

  after adding the dataset

  http://evdocs.medgenius.info/pictures/colored_strips_quick_start.png

Play around and then export the tree to pdf file

Try different display mode:

Then download the plot as PDF file: