Update the default values of partitionFinder parameters

iqtree · Apr 16, 2024 · d786299 · d786299
1 parent 49b264e
commit d786299
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Showing 2 changed files with 11 additions and 2 deletions.
diff --git a/main/phylotesting.cpp b/main/phylotesting.cpp
@@ -2008,9 +2008,18 @@ void testPartitionModel(Params &params, PhyloSuperTree* in_tree, ModelCheckpoint
 
     // 2017-06-07: -rcluster-max for max absolute number of pairs
     if (params.partfinder_rcluster_max == 0) {
-        params.partfinder_rcluster_max = max((size_t)1000, 10 * in_tree->size());
+        // params.partfinder_rcluster_max = max((size_t)1000, 10 * in_tree->size());
+        params.partfinder_rcluster_max = 10 * in_tree->size();
     }
 
+    // show the parameters for partition finder
+    cout << endl;
+    cout << "PartitionFinder's parameters:" << endl;
+    cout << part_algo << endl;
+    cout << "Percentage: " << params.partfinder_rcluster << endl;
+    cout << "Maximum pairs: " << params.partfinder_rcluster_max << endl;
+    cout << endl;
+
 	if (params.partition_merge != MERGE_NONE) {
         double p = params.partfinder_rcluster/100.0;
         size_t num_pairs = round(in_tree->size()*(in_tree->size()-1)*p/2);

diff --git a/utils/tools.cpp b/utils/tools.cpp
@@ -1127,7 +1127,7 @@ void parseArg(int argc, char *argv[], Params &params) {
     params.siteLL_file = NULL; //added by MA
     params.partition_file = NULL;
     params.partition_type = BRLEN_OPTIMIZE;
-    params.partfinder_rcluster = 100;
+    params.partfinder_rcluster = 10; // change the default from 100 to 10
     params.partfinder_rcluster_max = 0;
     params.partition_merge = MERGE_NONE;
     params.merge_models = "1";