+ }else if (globaldata->helpRequest == "tree.shared") {
+ cout << "The tree.shared command can only be executed after a successful read.otu command." << "\n";
+ cout << "The tree.shared command parameters are groups, calc, line and label. The calc parameter is required, and 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 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 << "There is no default value for calc." << "\n";
+ validCalcs->printCalc("treegroup", cout);
+ cout << "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "dist.shared") {
+ cout << "The dist.shared command can only be executed after a successful read.otu command." << "\n";
+ cout << "The dist.shared command parameters are groups, calc, line and label. The calc parameter is required, and 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 distance matrices created for, and are also separated by dashes." << "\n";
+ cout << "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example dist.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 and thetayc." << "\n";
+ validCalcs->printCalc("matrix", cout);
+ cout << "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "bootstrap.shared") {
+ cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n";
+ cout << "The bootstrap.shared command parameters are groups, calc, iters, line and label. The calc parameter is required, and 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 bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters)." << "\n";
+ cout << "Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
+ cout << "There is no default value for calc. The default for iters is 1000." << "\n";
+ validCalcs->printCalc("boot", cout);
+ cout << "The bootstrap.shared command outputs a .tre file for each calculator you specify at each distance you choose containing iters number of trees." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ }else if (globaldata->helpRequest == "concensus") {
+ cout << "The concensus command can only be executed after a successful read.tree command." << "\n";
+ cout << "The concensus command has no parameters." << "\n";
+ cout << "The concensus command should be in the following format: concensus()." << "\n";
+ cout << "The concensus command output two files: .concensus.tre and .concensuspairs." << "\n";
+ cout << "The .concensus.tre file contains the concensus tree of the trees in your input file." << "\n";
+ cout << "The branch lengths are the percentage of trees in your input file that had the given pair." << "\n";
+ cout << "The .concensuspairs file contains a list of the internal nodes in your tree. For each node, the pair that was used in the concensus tree " << "\n";
+ cout << "is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages." << "\n" << "\n";