Bản mẫu: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).

**Đặc điểm cơ bản**

**Cách sử dụng**
tạo ra
tạo ra
tạo ra
Note that the order of the parameters does not matter. Exactly the same output is produced by

**Nền màu kỹ thuật**
The clade template has many features for customising the appearance. Using them optimally requires some understanding of how the template works. The cladogram is constructed using nested HTML tables and the lines of the cladogram are borders of the cells ( tags). Each clade template creates an HTML table with the elements show as follows:
Replace LeafA with another clade structure.A second HTML table is placed inside a the right-hand cell of the outer table.

sublabelA

**Kiểu các dấu ngoặc và các nhánh**
The appearance of the cladogram can be customised by changing the border attributes of the HTML cell elements, using the parameters state, color and thickness as shown below:

**Clade ngược lại**
The cladograms can also be generated right to left using cladeR, as shown below.
While this has limited value in English Wikipedia, it can be useful for presenting alternative phylogenies, e.g. as in the following example:

**Dữ liệu ở định dạng Newick**
A common method of presenting phylogenetic data is to use the Newick format. Many published papers provide data in Newick format in their supplementary materials and several taxonomic and phyogenetic websites provide downloads (e.g. Open Tree of Life). These Newick strings can be used to generate cladograms in several ways.

**Chuỗi Newick như một tài nguyên**
Firstly, the Newick format data can be used to generate the clade structure markup using a text editor or one of several tools. 
The phylogenetic tree shown shown to the right is represented by the following Newick and Clade code- Newick format: ((a,b),(c,d))- Clade code: 
The manual procedure for conversion in a text editor is
# Replace "(" with 
# Edit to replace commas with pipes and numbers
# Edit clade labels if needed
Fortunately, there are a number of methods for automating this task. 
# One method is to use the NewickConverter template (see instructions therein).
#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.
#Example of a 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

**Sử dụng chuỗi Newick trực tiếp**
The Newick format data can also be added using the newickN, where N refers to the child node (as with other parameters).
For instance, the following Newick string
((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera
can be put in the clade code as in the following example:
The Newick format data provided Open Tree of Life and other sources typically has extraneous encoding data. This can be removed using the newickN-pattern and newickN-replace parameters which supply a Lua pattern (similar to Regex) and replacement. The following code uses Newick format data for the genus Prionailurus downloaded from using Open Tree of Life ( source data):
}}
tạo ra

**Sử dụng hộp**
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. You can use Cladogram to produce the box.

**Kiểm soát bố cục của chị em**
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.
Another 'trick' is to introduce a dummy clade. The red line in the following example shows where an extra clade has been inserted:
To achieve this, instead of
hiển thị dưới dạng:
sử dụng
which displays as:

**Nút dấu ngoặc và dán nhãn**

**Thêm thanh dọc và dấu ngoặc**
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.
Note the using of the non-breaking space ( ) to move the vertical bar from the leaf text. 
The horizontal lines can be omitted by using barN=colour throughout. Thus the following produces simple vertical bars:

**Màu dấu ngoặc định rõ**
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.

**Thêm nhãn văn bản vào dấu ngoặc**
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. A couple of methods are available.
# Text labels for each bracket/bar can be added using Barlabel (see instructions at template page). 
# Use the grouplabelN parameter. This adds a label to the right of the righthand bracket or bar, as shown in the following example. The right hand column illustrates how grouplabel adds an HTML cell to the right of the terminal leaf.
In the example above grouplabel was used to label a bar marking the entire clade. It provided an alternative to labelA. However, if the bar is only applied to some terminals, grouplabelN can be used to mark paraphyletic groups. The following example also demonstrates the use of grouplabelstyleN to apply CSS styling to the grouplabel, in this case the color.
The grouplabel parameter can be used to add multiple labels with the aid of the clade labels template. This template uses absolute CSS positioning to determine the placement of the label. When applied to a grouplabel1 parameter on the outer clade it behaves very similarly to barlabel. A simple example to label two groups is shown below:
The grouplabel parameter can contain any Wikitext or allowed HTML content and this offers a lot of flexibility in customising cladograms. The following example uses grouplabel to add an alternative topology using cladeR:
output1=
}}

**Gỡ lỗi**
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 leafbarN=colour for bar, e.g. 2=bar2=midnightblue.- You have only attempted to apply brackets/bars to leaf nodes.

**Hạn chế**

**Chiều dài nhãn**
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 &nbsp; not as actual spaces.- Line breaks (i.e. ) should not be used.

**Sự khác biệt của trình duyệt**
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, lc=yes, 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.

**Bao gồm trong sách**
There are many known bugs in rendering tables in the software which produces Wikipedia books; see the //meta.wikimedia.org/wiki/Book_tool/Feedback book tool feedback page.  these result in the lines in cladograms not displaying in books.

**Cladograms lớn**
There are limitations on the size and complexity of the cladograms which can be drawn:- A maximum of 20 children is allowed per node. - The Wikimedia software has certain limits on the processing allowed by templates and modules. Large cladograms can potentially exceed some of these limits.
** Post-expand include size. Essentially this is the output of all templates, modules and parser calls. Pages with very large or several large cladograms will occasionally exceed this limit, especially on larger pages with many references and other demands on the system.
** Template expansion depth limit. When a template is used it adds to the expansion depth, once for the template expansion and once for parameter expansion. As a result, template calls can only be nested 20 deep. Because cladograms are built by nesting templates within each other this is a common problem on larger phylogenetic trees. Fortunately there are now ways around this problem (see following section ).

**Kỹ thuật xây dựng cladograms lớn.**
Because cladograms are build by nesting clade templates within each other, larger cladograms can exceed the expansion depth allowed by the Wikimedia software. The cladogram on the right fails on the twentieth nested clade template.
There are two methods to get around this limitation: - the use of the clade sequential template and - the use of subtrees within the clade template. 

**Sử dụng danh sách tuần tự của đơn vị phân loại**
This approach uses the template clade sequential to list taxa in a taxonomic sequence. In the following example six taxa are listed sequentially in the template and the cladogram has the first one as the first branch, the second next and so on until the final two are sisters. Because all taxa are added in one template call, this only counts once towards the 20 limit. The downside is that it is not possible to format each level independently.
The second example shows that some substructure can be added to each level with normal use of the clade template.

**Sử dụng cây con**
This method uses the parameters target and subclade to "modularise" the phylogenetic tree. Each subtree is processed in parallel so they don't contribute to the expansion depth in an additive manner. The limit applies to each tree, but many subtrees can be used. 
The basic arrangement is illustrated below. The main tree has two subclades, A and B, and subclade B calls a third.