Newick Tree Formats

Newick Format

Newick format for trees was established June 24, 1986 as an product of a meeting at Newick's Seafood Restaurant during a meeting of the Society for the Study of Evolution. The format was designed for representing rooted trees with labled nodes and specified lengths between parent and child. The target audience of this representation is people interested in representing phylogenetic trees. Officially the tree ends in a semicolon (redundant since the parens must balance). The standard also does not allow length for the distance for a line leading to the root since this has no meaning in the context of plylogeny. Trees are represented as an annotated nested list of node names. Node names are a letter optionally followed by more letters, digits or an underline. Node names can be followed by a length separated from the name by a colon. For example

(ant:17, (bat:31, cow:22):7, dog:22, (elk:33, fox:12):40);

is thre tree with three leaves. The left child of the root is ant with a arc 17 long. The right child is branch 7 long with to an internal node with left and right branches of bat and cow respectively.

A rooted tree:

(dog:20, (elephant:30, horse:60):20):50

Here is an example from the phylip web site:

(
    (raccoon:19.19959,bear:6.80041):0.84600,
    (
        (sea_lion:11.99700, seal:12.00300):7.52973,
        (
            (monkey:100.85930,cat:47.14069):20.59201, 
            weasel:18.87953
        ):2.09460
    ):3.87382,
    dog:25.46154
);

and

(Bovine:0.69395,(Gibbon:0.36079,(Orang:0.33636,(Gorilla:0.17147,(Chimp:0.19268, Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460)

Optionally one can label internal nodes. For example:

((cow:12, gnu:10)bigThings:3, (ant:23, bat:19)smallThings:5);