(The RadCon Manual v1.1.3)

Newick Format

The Newick Format is a format for storing tree descriptions. A tree description is information about the structure of a tree.

The Phylip and NEXUS formats use the Newick Format.

Newick Format

The Newick Format was defined by an informal commitee of phylogenetic programmers meeting in Newick's lobster restaurant on the 24th of June 1986 (see Felsenstein,1993).

Newick Tree Descriptions

The hierarchical structure of trees means they can be efficiently represented as sets of nested paired parentheses.

An example Newick tree description

(((Cow, Lungfish), Salmon), Lamprey);

This tree description represents a tree with the four leaves Cow, Lungfish, Salmon and Lamprey. The innermost pair of parentheses specifies the sister group relationship of the Cow and Lungfish. The next most inclusive pair of brackets indicates that the Salmon groups with this pair to the exclusion of the Lamprey. The outermost pair of brackets groups all the leaves together and the semicolon indicates the end of the tree description.

Branch Lengths

Branch lengths are stored in Newick tree descriptions as real numbers following a colon which is placed immediately after the group descended from the branch to which the length refers.

An example Newick tree description with branch lengths

(((Cow:18.87953, Lungfish:7.93875):5.29292, Salmon:9.98944):11.50334, Lamprey:13.34753);

This tree description indicates that the branch to the Cow is of length 18.87953 and that the Salmon and Lungfish are separated by a distance of 9.98944 + 5.29292 + 7.93875 = 23.2211.

Line Breaks

Line breaks may occur at any time in a Newick tree description except in the middle of a leaf name or branch length.

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This page is maintained by Mark Wilkinson and was last modified February 15, 2007