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R2012a Documentation → Bioinformatics Toolbox
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Contents

Index

• Getting Started

• User's Guide

• Functions

• Constructor

• Data Formats and Databases

• Data Visualization

• Trace Tools

• Sequence Conversion

• Sequence Utilities

• Sequence Statistics

• Sequence Visualization

• Pairwise Sequence Alignment

• Multiple Sequence Alignment

• Scoring Matrices

• Phylogenetic Tree Tools

• Phylogenetic Tree Methods

cluster (phytree)

get (phytree)

getbyname (phytree)

getcanonical (phytree)

getmatrix (phytree)

getnewickstr (phytree)

• Graph Theory

• Graph Visualization Methods

• Gene Ontology

• Gene Ontology Methods

• Protein Analysis

• Profile Hidden Markov Models

• Microarray File Formats

• Microarray Utilities

• Microarray Data Analysis and Visualization

• Microarray Normalization and Filtering

• BioIndexedFile Methods

• BioRead Methods

• BioMap Methods

• GFFAnnotation Methods

• GTFAnnotation Methods

• HeatMap Methods

• Clustergram Methods

• ExpressionSet Methods

• ExptData Methods

• DataMatrix Methods

• MetaData Methods

• MIAME Methods

• Statistical Learning

• Mass Spectrometry

• Bioanalytics

Examples

• Release Notes

getbyname (phytree) - Branches and leaves from phytree object

Syntax

S = getbyname(Tree, Expression) S = getbyname(Tree, String) S = getbyname(Tree, String, 'Exact', ExactValue)

Arguments

`Tree`	phytree object created by `phytree` function (object constructor) or `phytreeread` function.
`Expression`	Regular expression or cell array of regular expressions to search for in `Tree`.
`String`	String or cell array of strings to search for in `Tree`.
`ExactValue`	Controls whether the full exact node name must match the string(s), ignoring case. Choices are `true` or `false` (default). When `true`, `S` is a numeric column vector indicating which node names match a query exactly, in full.

Description

S = getbyname(Tree, Expression) searches the nodes names in Tree, a phytree object, for the regular expression(s) specified by Expression. It returns S, a logical matrix of size NumNodes-by-M, where M is either 1 or the length of Expression. Each row in S corresponds to a node, and each column corresponds to a query in Expression. The logical matrix S indicates the node names that match Expression, ignoring case.

S = getbyname(Tree, String) searches the nodes names in Tree, a phytree object, for the string(s) specified by String. It returns S, a logical matrix of size NumNodes-by-M, where M is either 1 or the length of String. Each row in S corresponds to a node, and each column corresponds to a query in String. The logical matrix S indicates the node names that match String, ignoring case.

S = getbyname(Tree, String, 'Exact', ExactValue) specifies whether the full exact node name must match the string(s), ignoring case. Choices are true or false (default). When true, S is a numeric column vector indicating which node names match a query exactly, in full.

Examples

Read a phylogenetic tree file created from a protein family into a phytree object.
```
tr = phytreeread('pf00002.tree');
```
Determine all the mouse and human proteins by searching for nodes that include the strings 'mouse' and 'human' in their names.
```
sel = getbyname(tr,{'mouse','human'});
view(tr,any(sel,2));
```