Newick

Newick (also called Newick notation or the New Hampshire format) is a compact text notation for encoding rooted or unrooted trees, used almost universally in phylogenetics to represent evolutionary relationships among taxa. It was adopted in 1986 by James Archie, William Day, Joseph Felsenstein, Wayne Maddison, Christopher Meacham, F. James Rohlf, and David Swofford, building on a tree-drawing format Meacham had written in 1984 for Felsenstein's PHYLIP package. The name comes from the second standardization meeting, held at Newick's restaurant in Dover, New Hampshire. The underlying idea — that a nested-parenthesis string corresponds one-to-one with a tree — was already noted by the mathematician Arthur Cayley in 1857.

The data model is a tree with labeled leaves (tips), optional internal-node labels, and optional branch lengths (edge weights). The syntax is recursive: a subtree is either a leaf name, or a parenthesized, comma-separated list of child subtrees followed by an optional name; a branch length is written after a colon; the whole tree ends with a semicolon. For example, (A:0.1,B:0.2,(C:0.3,D:0.4):0.5); gives four tips, one internal clade, and distances to each parent node. Leaf names may be any printable string except blanks, colons, semicolons, parentheses, and square brackets, with underscores standing in for spaces. Square-bracketed comments carry ad-hoc annotation. Sibling order is not meaningful, so a single tree has many equivalent Newick strings.

Because it is small, human-readable, and trivially parsed, Newick is the default interchange format for phylogenetic tools such as ete3, Biopython, TreeGraph 2, and the phylogeny.fr and dendroscope ecosystems, and it is embedded inside the richer Nexus block format. Its strengths are simplicity and ubiquity; its limitations are real. There is no standard slot for edge (versus node) attributes, so bootstrap or support values are conventionally squeezed into internal-node labels — which then attach to the wrong branch after rerooting, a well-documented source of errors. It also cannot express reticulate structures like hybridization or gene flow, since a plain tree has no cross-links.

These gaps drove several successors. The New Hampshire X (NHX) extension adds [&&NHX:...] key-value tags in comments; Extended and Rich Newick add #-tagged hybrid nodes for phylogenetic networks; and the XML-based phyloXML and NeXML were designed to carry typed, edge-aware metadata that Newick cannot. For general graph work, converters such as newick_to_graphml map Newick trees into GraphML.