Update the default setting for parallelizing building an initial tree

Author: trongnhanuit

tree/tree.cpp

@@ -749,7 +749,7 @@ void cmaple::Tree::doPlacementTemplate(const int num_threads, std::ostream& out_
       // update the threshold to stop the search earlier if starting from placements found from the parallel search
       const int bk_failure_limit_sample = params->failure_limit_sample;
       if (parallel_search)
-          params->failure_limit_sample = 4;
+          params->failure_limit_sample = 3;
       for (size_t j = 0; j < current_chunk_size; ++j)
       {
           // increase i and move the sequence pointer

utils/tools.cpp

@@ -575,7 +575,7 @@ cmaple::Params::Params() {
   threshold_prob = 1e-8;
   mutation_update_period = 25;
   min_taxa_parallel_placement = 1000;
-  num_samples_per_thread = 3;
+  num_samples_per_thread = 5;
   upward_search_extension = 5;
   failure_limit_sample = 5;
   failure_limit_subtree = 4;