Module:Clade/doc

This module is designed to be used with the clade template to draw phylogenetic trees or cladograms. The new template-module combination extends the feature available with the clade and cladex templates, while replicating the behaviour of the older templates written with the template language. This module is copied from the test version Module:Sandbox/Jts1882/CladeN, which was used with the template Template:CladeN to test the features during development.

Additionally, the module has the code for template {{clade newick converter}}, which is a basic utility to convert Newick strings into nested clade structures. This is not to be used in wikipedia articles, but is a tool to help construct cladograms for inclusion in articles.

The diagram below gives an overview of the features. See the template documentation for a more detailed description of how to use the templates.

Usage

{{#invoke:Clade|main|style={{{style}}}}}

Examples

Simple examples mimicking the clade template:

Example demonstrating more advanced features of cladeN:

Example demonstrating features available:

Template:Clade
Node structure
label1

leaf 1

label2
label A

leaf A

label B

leaf B

 leaf 2 is a nested clade structure
label3

leaf 3

sublabel3 
|label1=Node structure  |sublabel1=(brackets)
|style1=background-color:#ffdddd;
|1={{Clade
   |label1=label1  
   |1=leaf 1             
   |label2=label2
   |grouplabel2= leaf 2 is a nested clade structure 
   |2={{Clade |style=background-color:#ffaaaa;
      |label1=label A
      |1=leaf A
      |label2=label B
      |2=leaf B
      |bar1=purple |bar2=purple 
      }}
   |label3=label3 |sublabel3=sublabel3
   |3=leaf 3           
   }}
(brackets)

 

Leaf styling
thicknessN

1 (default)

2

 line thickness

3

colorN

black (default)

red

blue

 #00ff00

stateN

solid (default)

dotted

dashed

 line styles

none

double 

|label3=Leaf styling  |sublabel3=(branches)
|style3=background-color:#eeeeee;
|3={{Clade
   |label1=thicknessN
   |1={{Clade
      |1=1 (default) |thickness1=1 |barbegin1=blue 
      |2=2           |thickness2=2 |bar2=blue |barlabel2= line thickness
      |3=3           |thickness3=3 |barend3=blue 
      }}
   |label2=colorN
   |2={{Clade
      |1=black (default) |color1=black          
      |2=red             |color2=red    
      |3=blue            |color3=blue   
      |4= #00ff00   |color4=#00ff00   
      }}
   |label3=stateN
   |3={{Clade
      |1=solid (default) |state1=solid  |barbegin1=purple 
      |2=dotted          |state2=dotted |bar2=purple 
      |3=dashed          |state3=dashed |bar3=purple |barlabel3= line styles
      |4=none            |state4=none   |bar4=purple
      |5=double          |state5=double |barend5=purple 
      }}
   }}
(branches)
node styling
thickness

I

J

K

color

A

B

C

state

X

Y

Z 

|label4=node styling  |sublabel4=(brackets)
|style4=background-color:#ffffee;
|4={{Clade
   |label1=thickness
   |1={{Clade |thickness=3
      |1=I  
      |2=J          
      |3=K             
      }}
   |label2=color
   |2={{Clade |color=red 
      |1=A
      |2=B                
      |3=C             
      }}
   |label3=state
   |3={{Clade |state=dashed
      |1=X 
      |2=Y         
      |3=Z        
   }} }}
(brackets)

 

newick
string

((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera

subtree
panthera

lion

jaguar

leopard

tiger

siberian

bengal

snow leopard

 expanded Newick string 
|label6=newick  
|style6=background-color:#ddffdd;
|6={{Clade
   |label1=string
   |1=((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera         
   |label2=subtree 
   |grouplabel2= expanded Newick string    
   |grouplabelstyle2=vertical-align: middle;
   |2={{Clade |style=background-color:#ccffcc;
      |newick1=((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera
      |1=Leaf1 (redundant if newick1 set)        
      }}
   }}
paraphyly example 
clade  label a paraphyletic group within a clade 
|label7=paraphyly example  |style7=background-color:#ffeeff;
|7={{Clade
   |1={{Clade
      |1=[[Geraniales]]          
      |2=[[Myrtales]]            
      }}
   |grouplabel2= label a paraphyletic group within a clade   
   |label2=clade
   |style2=background-color:#ffddff;
   |2={{Clade
      |1=[[Crossosomatales]]         |barbegin1=purple
      |2={{Clade
         |1=[[Picramniales]]         |bar1=purple
         |2={{Clade
            |1=[[Sapindales]]        |bar1=purple 
            |2={{Clade
               |1=[[Huerteales]]     |bar1=purple
               |2={{Clade
                  |1=[[Brassicales]] |barend1=purple
                  |2=[[Malvales]]    |style2=background-color:#ff99ff;
   }} }} }} }} }} }}

A cladogram illustrating clade features.


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