- string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile,line, label;
- string cutoff, format, precision, method, fileroot, iters, jumble, freq, single, rarefaction, shared, summary, sharedsummary, sharedrarefaction;
+ string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
+ string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund;
+