phytreeread

Read phylogenetic tree file

Syntax

Tree = phytreeread(File)
[Tree, Boot]= phytreeread(File)

Input Arguments

File

Newick-formatted tree files (ASCII text file). Enter a file name, a path and file name, or a URL pointing to a file. File can also be a MATLAB® character array that contains the text for a file.

Output Arguments

Tree

phytree object created with the function phytree.

Boot

Column vector of bootstrap values for each tree node specified in File. If File does not specify a bootstrap value for a node, it returns a NaN value for that node. phytreeread considers the following values in File to be bootstrap values:

  • Values within square brackets ([]) after the branch or leaf node lengths

  • Values that appear instead of branch or leaf node labels

Description

Tree = phytreeread(File) reads a Newick-formatted tree file and returns a phytree object containing data from the file.

The NEWICK tree format can be found at

http://evolution.genetics.washington.edu/phylip/newicktree.html

    Note:   This implementation allows only binary trees. Non-binary trees are translated into a binary tree with extra branches of length 0.

[Tree, Boot]= phytreeread(File) returns Boot, a column vector of bootstrap values for each tree node specified in File. If File does not specify a bootstrap value for a node, it returns a NaN value for that node. phytreeread considers the following values in File to be bootstrap values:

  • Values within square brackets ([]) after the branch or leaf node lengths

  • Values that appear instead of branch or leaf node labels

Examples

tr = phytreeread('pf00002.tree')

 Phylogenetic tree object with 33 leaves (32 branches)

More About

Was this topic helpful?