getnewickstr

Create Newick-formatted character vector

Syntax

nwk = getnewickstr(Tree)
getnewickstr(..., 'PropertyName', PropertyValue,...)
getnewickstr(..., 'Distances', DistancesValue)
getnewickstr(..., 'BranchNames', BranchNamesValue)


Arguments

Tree	Phytree object created with the function phytree.
DistancesValue	Property to control including or excluding distances in the output. Enter either true (include distances) or false (exclude distances). Default is true.
BranchNamesValue	Property to control including or excluding branch names in the output. Enter either true (include branch names) or false (exclude branch names). Default is false.

Description

nwk = getnewickstr(Tree) returns the Newick-formatted character vector of a phylogenetic tree object (Tree).

getnewickstr(..., 'PropertyName', PropertyValue,...) defines optional properties using property name/value pairs.

getnewickstr(..., 'Distances', DistancesValue), when DistancesValue is false, excludes the distances from the output.

getnewickstr(..., 'BranchNames', BranchNamesValue), when BranchNamesValue is true, includes the branch names in the output.

Examples

1. Create some random sequences.

   seqs = int2nt(ceil(rand(10)*4));

2. Calculate pairwise distances.

   dist = seqpdist(seqs,'alpha','nt');

3. Construct a phylogenetic tree.

   tree = seqlinkage(dist);  

4. Get the Newick-formatted character vector.

   nwk  = getnewickstr(tree) 

References

Information about the Newick tree format.

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

Version History

Introduced before R2006a