Main Content

phytreeread

Read phylogenetic tree file

Syntax

Tree = phytreeread(File)
Tree = phytreeread(File,'TimeOut',TimeOutValue)
[Tree, Boot]= phytreeread(File)

Input Arguments

File

Character vector or string specifying a Newick- or Nexus-formatted tree file (ASCII text file) name, a path and file name, or a URL pointing to a file.

For the Nexus tree format, only one tree from the first TREES block is read. This is either the last default tree (marked by an asterisk *) or the first tree, if no default trees exist.

TimeOutValueConnection timeout in seconds, specified as a positive scalar. The default value is 5. For details, see here.

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 (for Newick-formatted trees only)

  • Values that appear instead of branch or leaf node labels (for both Newick- and Nexus-formatted trees)

Description

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

Tree = phytreeread(File,'TimeOut',TimeOutValue) sets the connection timeout (in seconds) to read data from a remote file or URL.

The NEWICK tree format can be found at:

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

The NEXUS tree format can be found at: 

https://wiki.christophchamp.com/index.php/NEXUS_file_format

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 (for Newick-formatted trees only)

  • Values that appear instead of branch or leaf node labels (for both Newick- and Nexus-formatted trees)

Examples

tr = phytreeread('pf00002.tree')

 Phylogenetic tree object with 33 leaves (32 branches)
tr2 = phytreeread('pf00002.nex')
Phylogenetic tree object with 33 leaves (32 branches)

Version History

Introduced before R2006a

See Also

| | |