Template:Clade/demo

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< Template:Clade
Revision as of 14:26, 7 November 2019 by imported>Jts1882 (updates)
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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 3 is a nested clade structure 
         |labelstyle2=background-color:#ffdddd;vertical-align:middle;
      |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    
      |labelstyle2=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 

Geraniales

Myrtales

clade

Crossosomatales

Picramniales

Sapindales

Huerteales

Brassicales

Malvales

 label a paraphyletic group within a clade
   |label7=paraphyly example 
   |style7=background-color:#ffeeff;
   |7={{Clade
      |1={{Clade
         |1=[[Geraniales]]          |state1=dashed
         |2=[[Myrtales]]            |state2=dotted
         }}
      |grouplabel2= label a paraphyletic group within a clade   
      |labelstyle2=vertical-align:middle;
      |label2=clade
      |style2=background-color:#ffddff;
      |2={{Clade
         |1=[[Crossosomatales]]         |barbegin1=purple
         |state1=double
         |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.