- ListVector* listOfNames;
- ReadOTUFile* read;
- InputData* input;
- FastaMap* fasta;
- string filename, fastafile, namesfile;
+ GroupMap* groupMap;
+ ReadMatrix* readMatrix;
+ FormatMatrix* formatMatrix;
+ NameAssignment* nameMap;
+ CountTable ct;
+ string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, countfile, columnfile, distFile, format, outputDir, groups, method;