# Glossary

## NEXUS

A file in NEXUS format store the strings in the data block as follows:

#NEXUS
Begin data;
Dimensions ntax = 3 nchar = 94;
Format datatype = nucleotide gap = - missing = ?;
Matrix
Taxon1 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGAAAAAAAAGTACATGATAAAACATCTGGTTTGGGCAAGATCGGAG
Taxon2 AGCGGGAAAAAATTAGATTCATGGGAGAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATNNNNNNNNNNNNNTTGGCCGCTNNN---GAG
Taxon3 ACTGGGACAATTACAACCAGCTCTTCGGTTAAGGCCAGGGTCCAGACAGGAACAGAATTCGGTTAAGGCCAGGGCTTAGATCATTATAT-----
;
End;


Note that NEXUS is the alignment format, i.e. all sequences must be the same length ('N' as unknown character or "-" as gap also counts) and correspond the nchar.

NEXUS file may contain additional blocks besides data. Each block starts with BEGIN block_name; and finishes with END;

For example, TREES block contains phylogenetic trees for the data using the Newick format, e.g. ((A,B),C);

#NEXUS
Begin trees;
Tree tree1= (fish,(frog,(snake, mouse)));
End;


A formal detailed description of the NEXUS format can be found in Maddison et al. (1997).