A simple NEXUS file (Maddison et al. 1997) containing the data for the example in Figure 5. The file consists of blocks, each holding a single kind of information, delimited by the markers BEGIN block_name; and END;. The taxa block lists the manuscripts appearing in the file. The characters block specifies the number of characters and the format in which readings are coded, listing the coded characters in the MATRIX section. The first three characters are parsimony-informative because each state ('a' and 'b') occurs in at least two manuscripts. The last two characters are parsimony-uninformative, because in each case the state 'b' only occurs in one manuscript.
#NEXUS BEGIN taxa; DIMENSIONS NTAX=4; TAXLABELS  MS_1  MS_2  MS_3  MS_4 ; END; BEGIN characters; DIMENSIONS nchar=5; FORMAT datatype=standard symbols="a b" labels ; MATRIX MS_1 aaaba MS_2 abaaa MS_3 bbbaa MS_4 babab ; END;