Difference between revisions of "Template:Clade"

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

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

produces

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

produces

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

produces

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

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: <source lang="perl"> 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/\(\Q$clade\E\)/${\join(,)}/; # substitute } pos($tree)=0; } $tree=~s/(\t*)\t\}\}/$1\}\}/g; # lazy fix

print $tree; </source>

Using a box

You can nest the templates and use links around the text. You may use non-breaking spaces (&nbsp;) 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.