spond

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

spond

Multiple trees on a single page

spond

/* 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*/

spond

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

spond

/* 

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 (spond@ucsd.edu)
Art FY Poon				 (apoon@ucsd.edu)
Simon DW Frost			 (sdfrost@ucsd.edu)

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Plot site-by-site estimates of dN-dS from FUBAR .csv files

Take the output (main .CSV) of FUBAR, and create a D3 plot over sites. Optionally, partition the plot into chunks of different color (e.g. gene/genome regions), and annotate them with horizontal bars.

spond

Annotated tree

An example that shows how to use styling call-backs to

1. Color terminal branches based on an externally supplied annotation (cluster assignment)
2. Adjust thickness of interior branches based on their bootstrap support
3. Label interior nodes (for the cladogram layout) with bootstrap values

spond

Compare the results of MEME and MEME-internal on the same dataset

The two charts show mean ω (internal branches only, for MEME-internal, and the entire tree for MEME) over sites. Sites with evidence for episodic diversifying selection are shown as circles along the x-axis.

spond

Compare the results of MEME and MEME-internal on the same dataset

The table shows any site which was found significant (p ≤ 0.05) by either version of MEME.

spond

How to add custom context menu items to tree nodes

This is accomplished via a call to d3_add_custom_menu which adds a menu to a specific node with callback defining

1. What text is displayed (based on the node object and associated data)
2. What happens on click (pass nodes and other data through transitive closure, because standard d3 .on handlers will be called on the menu item, not the node object).
3. When the menu item is shown (a boolean callback based on the node object and associated data)