Newick

Newick format, also known as the Newick tree format, is a simple ASCII notation used to encode hierarchical trees, especially phylogenetic trees. A tree is described by nested parentheses that group child nodes; leaves are labeled, and internal nodes can be labeled or left unnamed. Each edge length is indicated after a colon preceding the next node. The complete tree ends with a semicolon.

The basic syntax uses parentheses to denote groupings, commas to separate siblings, and colons to specify branch lengths. Example: ((A:0.1,B:0.2):0.3,(C:0.4,D:0.5):0.6);

Origin and usage: It became a de facto standard in phylogenetics and is supported by many programs and libraries, including PHYLIP, PAUP*, MEGA, Biopython's Phylo, R's ape and phangorn, DendroPy, and the ETE toolkit.

Extensions and limitations: Extended Newick and Rich Newick variants allow annotations such as bootstrap values and node labels; however, there is no single universal metadata standard beyond branch lengths, and the format is primarily designed for rooted or unrooted trees with a flexible, but binary, structure. It remains valued for its compactness and broad software support, though for more complex metadata or multiple trees per file, alternative formats like NEXUS or more expressive schemas may be used.