From Latin nexus 'connection'.

Nexus is a common data format for character data. An example of a simple Nexus formatted file with four manuscripts (taxa) and five characters is as follows:

begin data;
    dimensions ntax=4 nchar=5;
    Ms1        AABAB
    Ms2        AABAC
    Ms3        ABABA
    Ms4        AAABD

This means that the first word, encoded as A in the first character of each of the character sequence, is common to all four manuscripts. The second word has a common variant, encoded as A, in manuscripts Ms1, Ms2, and Ms4, but a different variant, B, in manuscript Ms3, and so forth.

Nexus files can be processed using common phylogenetic programs such as PAUP*, Phylip, and Stemmaweb.


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