ReadMatrix* readMatrix;
FormatMatrix* formatMatrix;
NameAssignment* nameMap;
- string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format;
+ string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir;
ofstream out;
ifstream in, inNames, inRow;
bool abort, allLines, groupError, large;