phytreewrite
Write phylogenetic tree object to Newick-formatted file
Syntax
phytreewrite(File, Tree)
phytreewrite(Tree)
phytreewrite(..., 'Distances', DistancesValue,
...)
phytreewrite(..., 'BranchNames', BranchNamesValue,
...)
Arguments
File | Character vector or string specifying a Newick-formatted file (ASCII text file) name, a path and file name, or a URL pointing to a file. |
Tree | Phylogenetic tree object, either created with phytree (object constructor function) or
imported using the phytreeread function. |
Description
phytreewrite( copies
the contents of a File, Tree)phytree object from the MATLAB® workspace
to a file. Data in the file uses the Newick format for describing
trees.
phytreewrite( opens
the Save Phylogenetic Tree As dialog box for you to enter or select
a file name.Tree)
phytreewrite(..., ' calls PropertyName', PropertyValue,
...)phytreewrite with optional
properties that use property name/property value pairs. You can specify
one or more properties in any order. Enclose each PropertyName in
single quotation marks. Each PropertyName is
case insensitive. These property name/property value pairs are as
follows:
phytreewrite(..., 'Distances', specifies whether to exclude the distances from the
output. DistancesValue,
...)DistancesValue can be true (default)
or false.
phytreewrite(..., 'BranchNames', specifies whether to exclude the branch names from
the output. BranchNamesValue,
...)BranchNamesValue can be true (default)
or false.
Examples
Read tree data from a Newick-formatted file.
tr = phytreeread('pf00002.tree')
Phylogenetic tree object with 33 leaves (32 branches)Remove all the mouse proteins and view the pruned tree.
ind = getbyname(tr,'mouse'); tr = prune(tr,ind); view(tr)
Write pruned tree data to a file.
phytreewrite('newtree.tree',tr)Version History
Introduced before R2006a
