phytreeread

Read phylogenetic tree file

Syntax

Tree = phytreeread(File)
[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.

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.

The NEWICK tree format can be found at:

The NEXUS tree format can be found at:

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)

Introduced before R2006a