This template is an eXtended version of {{Clade}}, hence the name. Both templates are for drawing branching trees with the node and base labels being clickable links. Such diagrams are especially suited to represent evolutionary trees (cladograms).
Most of the documentation is the same as the parent template, {{Clade}}, and is included below for convenience. Unless the two extra features of {{Cladex}} are needed, you are advised to use {{Clade}}.
The two extra features of {{Cladex}} are:
Double lines leading to a node can be produced as easily as dotted lines.
Brackets or bars of a chosen colour can be placed to the right of a set of leaf nodes in the cladogram, thus allowing paraphyletic groups to be identified. See #Bracketting nodes. Text labels for these brackets/bars can be provided using {{Barlabel}}.
{{Clade}} and {{Cladex}} can be freely mixed, so if only some clades require the extra features, only these need be specified using {{Cladex}}.
{{Cladex}} only. To replace a single line leading to the Nth child by a double line, use |stateN=double. Notice that {{Cladex}} has only been used for the (sub)clade where the double line is wanted. The outermost clade should always be specified with {{Clade}} unless its style is altered — see further.
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.
useconstantN=>"\n";useconstantT=>"\t";my$tree='((a,b),(c,d));';# get sequence$tree=~s/[\n\r]//g;# loose those spaces$tree=~s/\:[\.\d]+//g;# loose those lengthswhile($tree=~m/\(/){foreachmy$clade($tree=~m/\(([^\(\)]+)\)/g){my@branches=split/\,/,$clade;s/(\t+)/$1\t/gfor@branches;die'ERROR: degenerate/empty node!'.Nif$#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\}\}/$1\}\}/g;# lazy fixprint$tree;
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.
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:
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.
The horizontal lines can be omitted by using |barN=colour throughout. Thus the following (note the use of |style=width:auto since the outermost clade uses the extra features of {{Cladex}}):
Note that brackets or bars must only be applied to leaf nodes. In the preceding example, it may be tempting to write
{{cladex|style=width:auto;font-size:85%;line-height:100%;
|1=Leaf A
|bar2=midnightblue
|2={{cladex
|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.
Either the outermost clade uses {{Clade}} or if it has to use {{Cladex}}, then |style=width:auto is present.
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.
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 சனவரி 2017[update], 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.
There are limitations on the size and complexity of the cladograms which can be drawn:
A maximum of 17 children is allowed per node. It may seem that this could easily be increased by editing the template, but see the next point.
Cladograms can only be expanded up to a certain level of complexity because the MediaWiki software limits the resources available for template expansion. The cladogram at APG III system#Phylogeny has had to be broken into three parts, because the entire cladogram exhausts the allowed resources (in this case the allowed expansion depth). Any change to the template could result in large cladograms failing to display correctly. In general, don't exceed a depth of 19, i.e. don't nest one cladex template inside another more than 19 times.
There are many known bugs in rendering tables in the software which produces Wikipedia books; see the book tool feedback page. As of சூலை 2011[update] these result in the lines in cladograms not displaying in books.
