get (phytree)

Retrieve information about phylogenetic tree object

Syntax

[Value1, Value2,...] = get(Tree, 'Property1','Property2',...)
get(Tree)
V = get(Tree)

Arguments

TreePhytree object created with the function phytree.
NameProperty name for a phytree object.

Description

[Value1, Value2,...] = get(Tree, 'Property1','Property2',...) returns the specified properties from a phytree object (Tree).

Properties for a phytree object are listed in the following table.

PropertyDescription
NumLeavesNumber of leaves
NumBranchesNumber of branches
NumNodesNumber of nodes (NumLeaves + NumBranches)
PointersBranch to leaf/branch connectivity list
Distances Edge length for every leaf/branch
LeafNamesNames of the leaves
BranchNamesNames of the branches
NodeNamesNames of all the nodes

get(Tree) displays all property names and their current values for a phytree object (Tree).

V = get(Tree) returns a structure where each field name is the name of a property of a phytree object (Tree) and each field contains the value of that property.

Examples

  1. Read in a phylogenetic tree from a file.

    tr = phytreeread('pf00002.tree')
    
    Phylogenetic tree object with 33 leaves (32 branches)
  2. Get the names of the leaves.

    protein_names = get(tr,'LeafNames')
    
    protein_names = 
    
        'Q9YHC6_RANRI/126-382'
        'VIPR1_RAT/140-397'
        'VIPR_CARAU/100-359'
         ...

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