Template:Clade/doc

This template is used for drawing branching trees with the node and base labels being clickable links. Such diagrams are especially suited to represent evolutionary trees (cladograms).

Features previously included only in a separate template, {{Cladex}}, are now incorporated in this template; {{Cladex}} should no longer be used.

Basic features

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

Note that the order of the parameters does not matter. Exactly the same output is produced by

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

	Subtree1 Leaf1   Subtree2 Leaf2

Styling brackets and branches

Description	Template code	Resulting output
Styling brackets The thickness, colour and state (solid, dashed, etc) of bracket lines can be changed using the thickness=, |color= and |state= parameters.	{{clade |label1=Bracket styling |sublabel1=(no suffix) |style1x=background-color:#ffffee; |1={{Clade |label2=color |2={{Clade |color=red |1=A |2=B |3=C }} |label1=thickness |1={{Clade |thickness=3 |1=I |2=J |3=K }} |label3=state |3={{Clade |state=dashed |1=X |2=Y |3=Z }} }} }}	Bracket styling thickness   I     J     K     color   A     B     C     state   X     Y     Z     (no suffix)
Styling individual branches The thickness, colour and state of individual branch lines can be changed using the thicknessN=, |colorN= and |stateN= parameters, where N is the number of the branch to be styled.	{{clade |label1=Branch styling |sublabel1=(append branch number) |style1x=background-color:#eeeeee; |1={{Clade |label2=colorN |2={{Clade |1=black (default) |color1=black |2=red |color2=red |3=blue |color3=blue |4= #00ff00 |color4=#00ff00 }} |label1=thicknessN |1={{Clade |1=1 (default) |thickness1=1 |2=2 |thickness2=2 |3=3 |thickness3=3 }} |label3=stateN |3={{Clade |1=solid (default) |state1=solid |2=dotted |state2=dotted |3=dashed |state3=dashed |4=none |state4=none |5=double |state5=double }} }} }}	Branch styling thicknessN   1 (default)     2     3     colorN   black (default)     red     blue      #00ff00     stateN   solid (default)     dotted     dashed     none     double     (append branch number)

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

Alternatively, one can easily generate required clade code by downloading the free Windows utility, 'Claded', via link at http://code.google.com/p/claded, 'Claded' allowing editing of Cladograms using a tree control.

{{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. You can use {{Cladogram}} to produce the box. Template:Cladogram

{{cladogram|title=Example
|caption=Sample of {{tl|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]]
                    }}
                }}
            }}
        }}
    }}
}}

Controlling the layout of sisters

When one sister is represented as a leaf node and the other as a labelled subclade, they do not appear to be at the same level. Consider this cladogram:

	Banksia subser. Sphaerocarpae (5 taxa)   Banksia subser. Leptophyllae   Banksia telmatiaea     (4 other taxa)

Although Banksia subser. Sphaerocarpae and Banksia subser. Leptophyllae are sisters, their names are not aligned in the cladogram. If this is considered undesirable, one solution is to use a label in both cases, as shown hereafter, which now shows the sisters at the same level.

	Banksia subser. Sphaerocarpae (5 taxa)   Banksia subser. Leptophyllae   Banksia telmatiaea     (4 other taxa)

Another 'trick' is to introduce a dummy clade. The dotted line hereafter shows where an extra clade has been inserted:

	Banksia subser. Sphaerocarpae (5 taxa)     Banksia subser. Leptophyllae   Banksia telmatiaea     (4 other taxa)

To achieve this, instead of

{{clade
 |1=Sister1
 |label2=Sister2
 |2={{clade
   |1=taxon1
   |2=taxon2}}
}}

which displays as:

	Sister1
Sister2	taxon1     taxon2

use

{{clade
 |1=Sister1
 ''|2={{clade'' (extra ''dummy'' clade)
   |label1=Sister2
    |1={{clade
       |1=taxon1
       |2=taxon2}}
   }}
}}

which displays as:

	Sister1
	Sister2   taxon1     taxon2

{{#ifeq:cladex|cladex|

Bracketting nodes

To insert a coloured 'bracket' around a set of leaf nodes which follow one another in the generated cladogram:

• Add barbeginN=colour for the first leaf node, where N is the order of that leaf node within its clade, and colour is the required colour.
• Add barN=colour for the remaining nodes other than the last (note that N must be the order of that node within its clade).
• Add barendN=colour for the last node.

|style=width:auto must be present.

{{clade|style=font-size:85%;line-height:100%;
|1={{clade
   |1=Leaf A
   |2=Leaf B|barbegin2=green
   |3=Leaf C|bar3=green
   |4={{clade
      |1=Leaf D|barend1=green
      |2=Leaf E
      |3=Leaf F|barbegin3=purple
      |4={{clade
         |1=Leaf G|bar1=purple
         |2=Leaf H|barend2=purple
         }}
      }}
   }}
}}

produces

	Leaf A     Leaf B       Leaf C         Leaf D       Leaf E     Leaf F         Leaf G       Leaf H

The horizontal lines can be omitted by using |barN=colour throughout. Thus the following (note the use of |style=width:auto):

{{clade|style=width:auto;font-size:85%;line-height:100%;
|1=Leaf A
|2={{clade
   |1=Leaf B|bar1=midnightblue
   |2=Leaf C|bar2=midnightblue
   }}
|3=Leaf D|bar3=midnightblue
}}

produces

	Leaf A
	Leaf B       Leaf C
	Leaf D

Note that brackets or bars must only be applied to leaf nodes. In the preceding example, it may be tempting to write

{{clade|style=width:auto;font-size:85%;line-height:100%;
|1=Leaf A
|bar2=midnightblue
|2={{clade
   |1=Leaf B
   |2=Leaf C
   }}
|3=Leaf D|bar3=midnightblue
}}

with the expectation that the bar will be to the right of the whole of the clade containing Leaf B and Leaf C. This does not produce the required output.

Specifying colours

You can use any of the ways in which colours can be specified in HTML; e.g. the standard colour names, the three or six hex digit notations, such as #FC3 or #F3C630, or the rgb() notation.

Supplying text labels

Text labels for each bracket/bar can be added using {{Barlabel}}. Accessibility guidelines require pages not to rely on colour alone, so it's particularly important to add labels if you have more than one bracket/bar and need to refer to them separately.

Debugging

If your cladogram doesn't display brackets/bars as you expected, check that:

• You understand the numbering system for the parameters barN, etc. The N must be the same as the number of the child within its clade. Thus typically you should write |N=label for leaf|barN=colour for bar, e.g. |2=[[Passeridae]]|bar2=midnightblue.
• You have only attempted to apply brackets/bars to leaf nodes.

Limitations

Label length

Labels produced by |labelN=, where N is 1, 2, ..., can lead to poor layout of the resulting cladogram. (This does not apply to the text of leaves, i.e. text produced by |N=.) To avoid problems:

• Labels should be kept as short as possible, ideally a single word
• Any necessary spaces in labels should be represented as   not as actual spaces.
• Line breaks (i.e. <br/>) should not be used.

Browser differences

Browser variation: left – most browsers; right – Safari

Cladograms are drawn by generating hidden tables. The horizontal and vertical lines making up the tree are actually the edges of table cells. The tables are then drawn by the browser or user agent using its internal algorithms. As these differ from browser to browser, the trees produced will not look the same on all browsers.

In particular, as of Template:MONTHNAME 2017, there are two algorithms for laying out tables with empty cells, used by two groups of browsers. Most browsers now use the algorithm that produces cladograms like the two on the left in the diagram. Safari (under both MacOS and iOS) uses another algorithm, producing cladograms like the two on the right in the diagram.

No automated "fix" for these differences exists at present.

If there is a choice over the ordering of the terminal nodes (leaves) of the tree, cladograms look best in a Safari-like browser if as much branching as possible is at the bottom of the cladogram. Typically this is produced by arranging the terminal nodes downwards on the page in order of their evolutionary divergence. Compare the bottom row of the diagram to the top row.

Large cladograms

There are limitations on the size and complexity of the cladograms which can be drawn:

• A maximum of 17 children is allowed per node.

Inclusion in books

There are many known bugs in rendering tables in the software which produces Wikipedia books; see the book tool feedback page. As of Template:MONTHNAME 2011 these result in the lines in cladograms not displaying in books.

Graphical summary

Template:Clade

Demo	Node structure label1 leaf 1   label2 leaf 2   label3 label A leaf A     label B leaf B      leaf 3 is a transcluded clade structure   (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       (branches) node styling thickness   I     J     K     color   A     B     C     state   X     Y     Z     (brackets) newick subtree panthera     lion     jaguar     leopard       tiger   siberian     bengal       snow leopard        expanded Newick string   string ((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera     paraphyly example      Geraniales     Myrtales     x   Crossosomatales         Picramniales         Sapindales         Huerteales         Brassicales       Malvales            paraphyletic group x
A cladogram illustrating clade template features.