Bioinformatics Toolbox™

getnewickstr (phytree) - Create Newick-formatted string

Syntax

String = getnewickstr(Tree)

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

Arguments

Description

String = getnewickstr(Tree) returns the Newick formatted string 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.

References

Information about the Newick tree format.

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

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 string.

   str  = getnewickstr(tree) 

See Also

Bioinformatics Toolbox functions: phytree (object constructor), phytreeread, phytreetool, phytreewrite, seqlinkage

Bioinformatics Toolbox methods of phytree object: get, getbyname, getcanonical

getmatrix (phytree)

getnodesbyid (biograph)