- cout << command << " is not a valid command in Mothur. Valid commands are read.dist(), read.otu(), read.tree(), cluster(), deconvolute(), collect.single(), collect.shared(), rarefaction.single(), rarefaction.shared(), summary.single(), summary.shared(), parsimony(), unifrac.weighted(), unifrac.unweighted(), quit(), help()." << endl;
+ cout << command << " is not a valid command in Mothur. Valid commands are ";
+ for (it = commands.begin(); it != commands.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;