Àdàkọ:Clade/doc

This template is used for illustrating branching trees with the nodes and base labels being clickable links. They are especially suited to represent evolutionary trees.

Usage

{{clade
|label1=Base
|1=Node
}}

produces

Base	Node

{{clade
|1={{clade
   |label1=[[Subtree1]]
   |1=Leaf1
   |label2=Subtree2
   |2=[[Leaf2]]
   }}
}}

produces

	Subtree1  Leaf1 Subtree2  Leaf2

{{clade| style=font-size:75%;line-height:75%
|1={{clade
   |label1=Subtree1
   |1=Leaf1
   |label2=Subtree2
   |2=Leaf2
   }}
}}

produces

	Subtree1 Leaf1 Subtree2 Leaf2

{{clade
|1={{clade
   |1={{clade | thickness=3
      |1=Leaf1
      |2=Leaf2
      }}
   |2=Leaf3
   }}
}}

produces

	Leaf1 Leaf2 Leaf3

To replace the solid line with a dashed line, use |stateN=dashed:

{{clade
|1={{clade
   |1={{clade
      |1=Leaf1|state1=dashed
      |2=Leaf2
      }}
   |2=Leaf3
   }}
}}

produces

	Leaf1 Leaf2 Leaf3

Tips

An easy way of creating larger cladograms is to use the Newick format and proceed to edit it using a suitable text editor to produce the markup.

1. Start with Newick format ((a,b),(c,d))
2. Replace "(" with "{{clade|"
3. Replace ")" with "}}"
4. Edit to replace commas with pipes and numbers
5. Edit clade labels if needed

{{clade
 |1={{clade
    |1=a
    |2=b
    }}
 |2={{clade
    |1=c
    |2=d
    }}
}}

Example Perl script to automate the conversion:

use constant N=>"\n";
use constant T=>"\t";

my $tree='((a,b),(c,d));'; # get sequence
$tree=~s/[\n\r]//g; # loose those spaces
$tree=~ s/\:[\.\d]+//g; # loose those lengths
while ($tree=~ m/\(/) {
	foreach my $clade ($tree=~ m/\(([^\(\)]+)\)/g) {
		my @branches=split /\,/,$clade;
		s/(\t+)/$1\t/g for @branches;
		die 'ERROR: degenerate/empty node!'.N if $#branches<1;
		$tree=~ s/\(\Q$clade\E\)/${\join('','{{clade',N,map(T.'|'.($_+1).'='.$branches[$_].N,0..$#branches),T.'}}')}/; # substitute
	}
	pos($tree)=0;
}
$tree=~s/(\t*)\t\}\}/$1\}\}/g; # lazy fix

print $tree;

Using a box

You can nest the templates and use links around the text. You may use non-breaking spaces ( ) to obtain spaces or to have labels that have spaces.

The entire cladogram can be placed in a box so that text flows nicely around it. Use within Template:Cladogram.

{{cladogram|title=Example
|caption=Sample of Template:Cladogram
|clades={{clade| style=font-size:75%;line-height:75%
|label1=[[Neornithes]]  
|1={{clade
	|label1=[[Paleognathae]]
	|1= 
	|label2= [[Neognathae]] 
	|2={{clade
	   |1=Other birds
	   |label1= 
	   |label2=[[Galloanserae]] 
	   |2={{clade
	       |1=[[Anseriformes]]
		   |label2=    
		   |2={{clade
		      |1=[[Galliformes]]
		      |2=[[Craciformes]]
		      }}
	      }}
	   }}
       }}
  }}
}}