- cout << "The tree.shared command creates a .tre to represent the similiarity between groups or sequences." << "\n";
- cout << "The tree.shared command can only be executed after a successful read.otu command or by providing a distance file." << "\n";
- cout << "The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision, line and label. You may not use line and label at the same time." << "\n";
- cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
- cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n";
- cout << "The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used. If you use a column file the name filename is required. " << "\n";
- cout << "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed." << "\n";
- cout << "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
- cout << "Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
- cout << "The default value for groups is all the groups in your groupfile." << "\n";
- cout << "The default value for calc is jclass-thetayc." << "\n";
- cout << "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose." << "\n";
+ mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n");
+ mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n");
+ mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision and label.\n");
+ mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
+ mothurOut("The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n");
+ mothurOut("The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used. If you use a column file the name filename is required. \n");
+ mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
+ mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
+ mothurOut("Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n");
+ mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ mothurOut("The default value for calc is jclass-thetayc.\n");
+ mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n");