NeXML - phylogenetic data as xml

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The future data exchange standard is here!

NeXML is an exchange standard for representing phyloinformatic data — inspired by the commonly used NEXUS format, but more robust and easier to process.

Process nexml data

Overview

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The NEXUS flat file format is a commonly used syntax for phylogenetic data. Unfortunately, over time, non-compliant NEXUS implementations have overloaded the standard - which has caused various problems. Meanwhile, mature technologies around the XML standard have emerged. These technologies have the potential to greatly simplify and improve robustness in the processing of rich phylogenetic data. This website is the home for the community-driven NeXML project, which seeks to leverage XML technologies in the development of a data standard that translates NEXUS concepts into a syntax that is more easily validated and processed. This approach promises several advantages:

Because of the advantages of NeXML over current standards, developers of phylogenetic software have come together as part of the NESCent working group for evolutionary informatics to develop this new data exchange standard based on XML technologies.

We have recently published a description of NeXML in Systematic Biology. If you use NeXML in your research, please consider citing doi:10.1093/sysbio/sys025

What are we doing about it?

NeXML development is being undertaken along a number of tracks:

Get involved!

If you are interested in being involved in the NeXML project in any way, please do! Here are some ways to get involved:

Acknowledgements

The research leading to these results has received funding from the [European Community's] Seventh Framework Programme ([FP7/2007-2013] under grant agreement n° [237046].

Suggested citation

Rutger A. Vos, J. P. Balhoff, J. A. Caravas, M. T. Holder, H. Lapp, P. E. Midford, A. Priyam, J. Sukumaran, X. Xia, and A. Stoltzfus. 2012. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology 61(4): 675-689 [doi:10.1093/sysbio/sys025]