Sergei Pond spond

Multiple trees on a single page

Different tree layouts.

In addition to linear/cladogram layouts, phylotree.js also implements a radial or cicrular layout. Invoking it is a matter of overriding the default setting.

It is important to set the radial option prior to binding Newick data to the tree, because at that time nodes are mapped to screen coordinates using current settings.

The layout mode can be changed after the tree has been rendered, but then it is

Non-interactive tree using phylotree.js

This is an example of using phylotree.js settings to create a tree which is suitable for a static display: no clickable nodes, nothing is selectable, fixed sizes in both dimensions.

The Newick string is loaded from a file using an asynchronous d3.text call.

The simplest example of using phylotree.js

Create a phylotree.js object from a Newick tree string, and display it in an SVG element using default settings and styles. Because the default tree view supports clickable nodes, it is necessary to include jQuery and Bootstrap. It is always necessary to include d3, and phylotree.js script and styles (unless overridden by the user).

Click on internal nodes to bring up menus that allow you to collapse/select them.

	/*

	THIS HyPhy BATCH LANGUAGE FILE IS PROVIDED AS AN EXAMPLE/TOOL FOR
	THE 2nd EDITION OF 'The Phylogenetic Handbook'

	Written by
	Sergei L Kosakovsky Pond ([email protected])
	Art FY Poon ([email protected])
	Simon DW Frost ([email protected])

	RequireVersion ("2.22");
	VERBOSITY_LEVEL = 1;

	// namespace 'io' for interactive/datamonkey i/o functions
	LoadFunctionLibrary("lib2014/IOFunctions.bf");

	// namespace 'utility' for convenience functions
	LoadFunctionLibrary("lib2014/UtilityFunctions.bf");

	io.displayAnalysisBanner ({"info" : "EDEPS is a modification of DEPS to look for directional evolution along all or

	/* 1. include a file to define the genetic code
	Note the use of base directory and path forming variables to make this analysis
	independent of directory placement
	*/

	/incFileName = HYPHY_LIB_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"TemplateModels"+DIRECTORY_SEPARATOR+"chooseGeneticCode.def"; /
	/* ExecuteCommands ("#include \""+incFileName+"\";"); */

	/* #include "functions.txt";/ /functions.txt has the genetic code*/