- cout << "The parsimony command can only be executed after a successful read.tree command, unless you use the randomtree parameter." << "\n";
- cout << "The parsimony command parameters are randomtree and iters. No parameters are required." << "\n";
- cout << "The parsimony command should be in the following format: parsimony(randomtree=yourRandomTreeValue, iters=yourIters)." << "\n";
- cout << "Example parsimony(randomtree=1, iters=500)." << "\n";
- cout << "The default value for randomTree is 0 (meaning you want to use the trees in your inputfile, randomtree=1 means you just want the random distribution of trees)," << "\n";
+ cout << "The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter." << "\n";
+ cout << "The parsimony command parameters are random and iters. No parameters are required." << "\n";
+ cout << "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, iters=yourIters)." << "\n";
+ cout << "Example parsimony(random=out, iters=500)." << "\n";
+ cout << "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony)," << "\n";