Comparison of file formats commonly used to represent trees. The features of various formats in common use are compared, with a square indicating support for a feature, and an open circle indicating partial or incomplete support. The Newick format represents trees (and no other information) as a series of parenthetical statements representing internal nodes, taxon names, and optionally branch lengths (as described in http://evolution.genetics.washington.edu/phylip/newicktree.html webcite). NEXUS  utilizes Newick strings, but also may store character information, processing commands (e.g., to exclude certain OTUs or characters), and notes. There is no formal way to propose extensions to NEXUS, but it has been widely adopted. PhyloXML  can store trees and molecular data, as well as accession numbers, geographic information, and other data. NeXML  is a different data format intended as an XML-based replacement for NEXUS. Both PhyloXML and NeXML have a formal syntax in an XSD schema. For further information, see .
Stoltzfus et al. BMC Research Notes 2012 5:574 doi:10.1186/1756-0500-5-574