Newick FormatEdit

Newick format is a compact, human-readable notation used to encode hierarchical trees in plain text. It is especially associated with the representation of phylogenetic trees, which are central to understanding evolutionary relationships among organisms. The syntax relies on parentheses to nest subtrees, colons to separate branch lengths, and semicolons to terminate a tree description. Because of its minimalism, Newick format has become a practical lingua franca for exchanging tree structures between software tools in the fields of phylogenetics and bioinformatics.

While remarkably simple, the format is purpose-built for trees and has influenced how researchers think about and manipulate phylogenetic tree data. It supports rooted and unrooted trees and allows optional labeling of leaves (taxa) and internal nodes, along with non-negative branch lengths that can encode time, amount of change, or other metrics. Over the years, Newick format has been extended and adapted to accommodate more complex data without losing backward compatibility, contributing to its enduring ubiquity in pipelines, databases, and software.

History

Newick format emerged in the mid- to late-20th century as researchers sought a plain-text, machine-readable way to store and exchange tree structures. The approach gained rapid traction because it is straightforward to parse, easy to generate, and broadly compatible with a wide range of programming languages and computational tools. As research moved toward large-scale phylogenomics, the format's simplicity remained a strength, even as users sought ways to annotate trees with additional information beyond branch lengths and basic labels. For more expressive needs, researchers turned to extensions and alternate formats that preserve the core Newick syntax while adding metadata.

Syntax and structure

A tree is written as a parenthesized expression, where each internal node groups its descendant subtrees. The root of the tree is the outermost group, and the entire tree ends with a semicolon.
Leaves are named as taxa, typically followed by a colon and a non-negative number representing the branch length from the leaf to its parent.
Internal nodes may also carry a label (a node name) after a closing parenthesis, and a colon followed by a branch length may follow that label.
Branch lengths are real numbers and are not required for all trees; a tree can be described with just topology (shape) and leaf names if needed.

Common patterns and a minimal example: - A simple rooted tree with three taxa might be written as: ((A:0.1,B:0.2):0.3,C:0.4); - Here, A and B share a more recent common ancestor than C. The numbers after the colons are branch lengths; the final semicolon terminates the description.

In practice, researchers often include additional annotations within or alongside the standard syntax, though doing so can reduce compatibility with tools that expect strict Newick. For readers who want to verify or test syntax, many bioinformatics resources provide parsers and validators that check for well-formed strings and interpret branch lengths.

Extensions and variants

Extended Newick and NHX (Newick with extra information) extend the expressive power of the basic format to carry additional metadata about nodes or branches, such as support values (bootstrap or posterior probabilities) and custom annotations, while keeping backward compatibility with standard parsers that ignore unknown annotations.
PhyloXML, NeXML, and NEXUS are alternative formats designed to carry richer metadata and reshaped data structures, often including detailed taxon information, character data, and provenance. These formats are chosen when downstream analyses require more expressive annotations than standard Newick can provide.
Some researchers use variant conventions to encode non-tree relationships or polytomies, but researchers should be mindful of tool support, as not all software can interpret non-standard extensions.

Tools and practical usage

Newick strings are produced, read, and transformed by a broad ecosystem of software. Examples include: - BioPython and other bioinformatics libraries that parse and manipulate trees. - ETE Toolkit and Dendroscope for visualization and editing of trees. - FigTree and other graphical tools for rendering publication-quality trees. - Analysis suites like MEGA and various phylogenetics pipelines that ingest Newick-formatted trees as part of larger workflows. - Many sequence analysis programs can export trees in Newick format to facilitate downstream visualization, annotation, or further computation, and can also import Newick strings produced by other tools.

Criticism and limitations

Newick format’s strength—the simplicity that makes it universally readable—also constitutes its main limitation. The standard representation captures topology and optional branch lengths, but it does not inherently encode rich metadata, provenance, or complex annotations in a portable, machine-readable way. For projects requiring detailed metadata, researchers often turn to alternative formats like PhyloXML, NeXML, or NEXUS; when rapid exchange of tree topology with lightweight data is the priority, Newick remains preferred for its compactness and broad support.

Another lingering issue is the representation of polytomies (nodes with more than two descendants) and uncertain relationships. While internal node labels and branch lengths can imply certain structures, explicit polytrees or non-binary relationships are sometimes more clearly expressed in extended or alternative formats. The trade-off between simplicity and expressiveness is a recurring theme in discussions about data standards in bioinformatics.