Nexus Format

NEXUS Format:

Nexus blocks are supported natively by several programs. In most cases, if a code accepts Nexus format, the preferred way to conduct analyses is through command blocks within the Nexus input file. Nexus files are difficult to parse because there are many format variations in use, and many different ways to encode the information. The tool NCLconverter is provided to help with this. Mark Holder created this tool for the CIPRES group, based on the NCL program of Paul Lewis. Each program here has its own philosophy and capabilities for Nexus interpretation. Accordingly, the documentation for each individual application should be the resource of first resort for issues that arise.

The original document specifying Nexus file formats is here [pdf].

IMPORTANT NOTE: Normalized Nexus will not be recognized by MrBayes 3.1.2

Normalized Nexus headers divide taxa and characters into separate groups, like this:
begin taxa;
dimensions ntax=12;
taxlabels a b c d e f g u v x y t; end

begin characters;
dimensions nchar=432;
format datatype=dna missing=?;

MrBayes 3.1.2 expects characters and taxa to be in a single data block, like this:

begin data;
dimensions ntax=12 nchar=432;
format datatype=dna missing=? gap=-;

This can be corrected manually with a text editor.

If there is a tool or a feature you need, please let us know.

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