//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
+ if (groups == "not found") { groups = ""; globaldata->Groups.clear(); }
else {
splitAtDash(groups, Groups);
globaldata->Groups = Groups;
//set users groups to analyze
util = new SharedUtil();
- util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted"); //sets the groups the user wants to analyze
+ util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze
util->getCombos(groupComb, globaldata->Groups, numComp);
if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }