In mathematics, Newick tree format (or Newick notation or New Hampshire tree format) is a way to represent graph-theoretical trees with edge lengths using parentheses and commas. It was created by James Archie, William H. E. Day, Joseph Felsenstein, Wayne Maddison, Christopher Meacham, F. James Rohlf, and David Swofford, at two meetings in 1986, the second of which was at Newick’s restaurant in Dover, New Hampshire, USA.
(,,(,)); *no nodes are named*
(A,B,(C,D)); *leaf nodes are named*
(A,B,(C,D)E)F; *all nodes are named*
(:0.1,:0.2,(:0.3,:0.4):0.5); *all but root node have a distance to parent*
(A:0.1,B:0.2,(C:0.3,D:0.4):0.5); *distances and leaf names* ***(popular)***
(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F; *distances and all names*
A; *a (degenerate) tree with one named node*
((B:0.2,(C:0.3,D:0.4)E:0.5)F:0.1)A; *a tree rooted on a leaf node* ***(rare)***
Newick format is typically used for tools like PHYLIP and is a minimal definition for a phylogenetic tree.
When an unrooted tree is represented in Newick notation, an arbitrary node is chosen as its root. Whether rooted or unrooted, typically a tree’s representation is rooted on an internal node and it is rare (but legal) to root a tree on a leaf node.
A rooted binary tree that is rooted on an internal node has exactly two immediate descendant nodes for each internal node. An unrooted binary tree that is rooted on an arbitrary internal node has exactly three immediate descendant nodes for the root node, and each other internal node has exactly two immediate descendant nodes. A binary tree rooted from a leaf has at most one immediate descendant node for the root node, and each internal node has exactly two immediate descendant nodes.
A grammar for parsing the Newick format:
| Note, * | ** separates alternatives. |
| Subtree –> Leaf | Internal |
| BranchSet –> Branch | Branch “,” BranchSet |
| Name –> empty | string |
| Length –> empty | ”:” number |
Whitespace (spaces, tabs, carriage returns, and linefeeds) within number is prohibited. Whitespace within string is often prohibited. Whitespace elsewhere is ignored.