Tree* TreeTools::MRPMultilabel(const vector<Tree*>& vecTr)
{
// matrix representation
VectorSiteContainer* sites = TreeTools::MRPEncode(vecTr);
// starting bioNJ tree
const DNA* alphabet = dynamic_cast<const DNA*>(sites->getAlphabet());
JCnuc* jc = new JCnuc(alphabet);
ConstantDistribution* constRate = new ConstantDistribution(1.);
DistanceEstimation distFunc(jc, constRate, sites, 0, true);
BioNJ bionjTreeBuilder(false, false);
bionjTreeBuilder.setDistanceMatrix(*(distFunc.getMatrix()));
bionjTreeBuilder.computeTree();
if (ApplicationTools::message)
ApplicationTools::message->endLine();
TreeTemplate<Node>* startTree = new TreeTemplate<Node>(*bionjTreeBuilder.getTree());
// MP optimization
DRTreeParsimonyScore* MPScore = new DRTreeParsimonyScore(*startTree, *sites, false);
MPScore = OptimizationTools::optimizeTreeNNI(MPScore, 0);
delete startTree;
Tree* retTree = new TreeTemplate<Node>(MPScore->getTree());
delete MPScore;
return retTree;
}
