NeXML

NeXML is an exchange standard for representing phylogenetic data|phylogenetic trees and networks, as well as associated data (e.g., alignments|alignments, phenotypes|phenotypes, geographical data|geographical data, annotations|annotations, etc.) in XML|XML. It is inspired by the commonly used NEXUS file format|NEXUS format, but uses a more robust mechanism for representing metadata. NeXML defines an ontology|ontology for describing phylogenetic data and their associated metadata, which allows users to add their own types of annotations to the data.

Overview

NeXML is a format for representing phylogenetic data in XML. It is designed to be easy to use, flexible, and capable of representing complex data structures. The format is based on the NEXUS format, but extends it with the ability to represent metadata in a more structured and flexible way.

Features

NeXML provides several features that make it a powerful tool for representing phylogenetic data:

• Metadata annotation: NeXML allows for the annotation of any element in the document with metadata. This metadata can be structured using the NeXML ontology, or any other ontology that the user chooses.

• Extensibility: Because NeXML is based on XML, it can be easily extended to represent new types of data or to incorporate new features.

• Interoperability: NeXML is designed to be interoperable with other data formats. It can be easily converted to and from other formats, and tools are available to facilitate this process.

• Validation: NeXML documents can be validated against a schema to ensure that they are correctly formatted. This helps to prevent errors and inconsistencies in the data.

Usage

NeXML is used in a variety of applications, including phylogenetic analysis, comparative genomics, and biodiversity informatics. It is supported by a number of software tools, including Mesquite, Bio::Phylo, and DendroPy.

See also

• PhyloXML
• NEXUS file format
• Comparison of software for molecular phylogenetics

External links

• NeXML website
• NeXML on GitHub

NeXML Resources
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