for(int i=0;i<numGroups;i++){
string tempNameFile = namefile + "." + toString(i) + ".temp";
+ if (outputDir == "") { outputDir = m->hasPath(fastafile); }
string tempDistFile = outputDir + m->getRootName(m->getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist";
//if there are valid distances