Sample output file. Output files are in the NEXUS format and ready to be input into PAUP or other programs that use this format. The indel characters have been added to the matrix and a table of correspondences is appended in the form of a comment, showing each indel character and the position of the indel upon which it is based. The Equate command allows 0 and 1 to be used, while maintaining the data type as 'DNA'. This allows one to perform maximum likelihood and other analyses that require this data type, though if a model of DNA substitution is applied, it may be most appropriate to exclude the indel characters from the analysis. They probably don't evolve according to the same model as substitutions.