Phyltree object (Comparative Genomics Toolbox for Matlab®)

Each field can be accessed by the dot (.) operation, or by the GET function. The GET function can work on multiple instances simultaneously. Most fields, except for those that are Dependent, can be modified using the dot (.) operation, or by the SET function.

	Field	Description	Type	Default	Dedicated Get/Set Function
	node_age	age of the node in year ago from present	double vector	[]
	l_node	Inherited from bintree. left-descendant of each node	double vector	[]
	r_node	Inherited from bintree. right-descendant of each node	double vector	[]
	parent	Inherited from tree. parent of each node	double vector	[]
	thd	Inherited from digraph. target-height-differences matrix	double matrix	[]
	name	Inherited from graph. name of object, should be short and used as identifier. This field will never be empty.	string	'unnamed'
	description	Inherited from graph. verbal description of the class content.	string	''
	source	Inherited from graph. verbal description of the source of information.	string	''
	type	Inherited from graph. type of graph.	string	'general graph'
	node_name	Inherited from graph. names of all nodes.	cell array of strings	{}	nodenames
	node_mass	Inherited from graph. mass of each node.	double vector	[]
	node_cfield	Inherited from graph. user-specific node customized fields.	cell array of values	{}
	node_cfield_name	Inherited from graph. names of node customized fields.	cell array of strings	{}
	weights	Inherited from graph. symmetric sparse weight matrix.	double matrix	[]
Dependent	no_nodes	Inherited from graph. number of nodes in the graph.	integer scalar	0	nonodes
Dependent	no_node_cfields	Inherited from graph. number of customized fields.	integer scalar	0
Dependent	no_edges	Inherited from graph. number of edges in the graph.	integer vector	0	noedges

Empty instance (scalar): an empty phyltree instance, with all fields initialized to their default values.; syntax: pt = phyltree;
Empty instance (matrix): an array of empty phyltree instances.; syntax: pt = phyltree(size,'size');
Copy constructor: one phyltree instance is copied into another.; syntax: pt_destination = phyltree(pt_origin);
Construction by field names: an instance is formed by directly providing field values. Any field which is not dependent is permitted.; syntax: pt = phyltree(field_name, field_value, ...);
Reading-in a file: an instance is formed by reading a file in PHYL or NEWICK formats.; syntax: pt = phyltree(filename);
Initialize a random phyltree: A random phyltree is built.; syntax: pt = phyltree('rand',no_leaves,time_span);

Computations:

balance: computes the balance vector. Source: digraph.
dag2code: finds the DAG-code of a DAG. Source: digraph.
gtd: computes the graph theoretic distance between two nodes. Source: bintree.
laplacian: computes the Laplacian of a graph. Source: graph.
vstruct: finds nodes that are center of a V-structure. Source: digraph.

Customized fields manipulations:

alloccfield: allocates a new customized field to a graph. Source: graph.
cfieldexist: finds whether a customized field exists in a graph. Source: graph.
cfieldnames: lists the customized fields in a GRAPH object. Source: graph.
getcfield: retrieves a customized field from a graph. Source: graph.
setcfield: sets values for a customized field of GRAPHs. Source: graph.

Display:

show: displays class content. Source: graph.

Evolutionary inference:

ardollo: makes Dollo ancestral reconstruction of binary characters.
computeevents: compute gain/loss/survive events of binary character.
dolloroot: finds the origin of a binary character.

I/O functions:

dump: writes a phylogenetic tree to disk.

Information extraction:

ancestors: finds the sequence of ancestors of a specifed node. Source: tree.
descendants: finds all descandants of a specifed node. Source: tree.
generation: computes the generation of each node.
iodegree: computes the in and out degrees of a digraph. Source: digraph.
iscomplete: tests whether the binary tree is fully connected. Source: bintree.
iscyclic: finds whether a DIGRAPH is cyclic or not. Source: digraph.
lca: finds the last common ancestor of a list of nodes. Source: tree.
leaves: finds these nodes that are leaves. Source: tree.
leavesunder: lists the leaves that are descendants of a particular node. Source: tree.
nodeid: finds the IDs of a list of nodes. Source: graph.
parents: finds the parents of specific nodes. Source: digraph.
root: finds the root of the tree. Source: tree.

Maintenance:

age2branchlength: computes branch lengths on a phylogenetic tree.
verify: computes missing. Source: bintree.

SET/GET functions:

get: get method
nodenames: retrieves the name of the nodes in the graph. Source: graph.
noedges: retrieves the number of edges in GRAPH objects. Source: graph.
nonodes: retrieves the number of nodes in GRAPH objects. Source: graph.
set: set method

Transformations:

addedge: adds an edge to a phylogenetic tree.
order: orders the nodes in a tree. Source: tree.
prunesubtree: prunes a subtree. Source: tree.
sampletree: samples the tree such as to keep a smaller number of leaves.
subtree: isolates the subtree branching from a certain node.
swap: replaces the indices of two nodes.
updatesubtree: substitutes the fields of a subtree in the father tree. Source: tree.

Visualization:

eigenproj: computes the eigenprojection of a graph. Source: graph.
view: plots a PHYLTREE