Nexus: An Extensible File Format for Systematic Information

TLDR

NEXUS is a file format intended to support future expansion, accommodate diverse data types, remain OS‑independent, and be easily processed by software. The format is modular, with files composed of standardized command blocks that separate public data (e.g., taxa, characters, trees) from private program‑specific data, and includes guidelines for reading, writing, and extending files. The paper provides a detailed description of the public block commands.

Abstract

NEXUS is a file format designed to contain systematic data for use by computer programs. The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program. To this end, the format is modular, with a file consisting of separate blocks, each containing one particular kind of information, and consisting of standardized commands. Public blocks (those containing information utilized by several programs) house information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc.; private blocks contain information of relevance to single programs. A detailed description of commands in public blocks is given. Guidelines are provided for reading and writing NEXUS files and for extending the format.