diff --git a/alignment/alignment.cpp b/alignment/alignment.cpp
index 51c38f37..9d1f7e19 100644
--- a/alignment/alignment.cpp
+++ b/alignment/alignment.cpp
@@ -128,7 +128,7 @@ int Alignment::checkAbsentStates(string msg) {
     if (!absent_states.empty())
         cout << "NOTE: State(s) " << absent_states << " not present in " << msg << " and thus removed from Markov process to prevent numerical problems" << endl;
     if (!rare_states.empty())
-        cerr << "WARNING: States(s) " << rare_states << " rarely appear in " << msg << " and may cause numerical problems" << endl;
+        cout << "WARNING: States(s) " << rare_states << " rarely appear in " << msg << " and may cause numerical problems" << endl;
     delete[] state_freq;
     return count;
 }
@@ -290,15 +290,15 @@ int Alignment::checkIdenticalSeq()
 				}
 			if (equal_seq) {
 				if (first)
-					cerr << "WARNING: Identical sequences " << getSeqName(seq1);
-				cerr << ", " << getSeqName(seq2);
+					cout << "WARNING: Identical sequences " << getSeqName(seq1);
+				cout << ", " << getSeqName(seq2);
 				num_identical++;
 				checked[seq2] = 1;
 				first = false;
 			}
 		}
 		checked[seq1] = 1;
-		if (!first) cerr << endl;
+		if (!first) cout << endl;
 	}
 	if (num_identical)
 		outWarning("Some identical sequences found that should be discarded before the analysis");
diff --git a/main/phylotesting.cpp b/main/phylotesting.cpp
index f44e80e0..e5bd22a6 100644
--- a/main/phylotesting.cpp
+++ b/main/phylotesting.cpp
@@ -1497,19 +1497,19 @@ void testPartitionModel(Params &params, PhyloSuperTree* in_tree, ModelCheckpoint
 
     // Analysis on supermatrix
     {
-        cout << "Performing single model on concatenated supermatrix..." << endl;
         Alignment *conaln = super_aln->concatenateAlignments();
         string model_name;
         switch (conaln->seq_type) {
-            case SEQ_DNA: model_name = "GTR+G"; break;
-            case SEQ_PROTEIN: model_name = "LG+G"; break;
-            case SEQ_CODON: model_name = "GY+G"; break;
+            case SEQ_DNA: model_name = "GTR+F+G"; break;
+            case SEQ_PROTEIN: model_name = "LG+F+G"; break;
+            case SEQ_CODON: model_name = "GY"; break; // too much computation, thus no +G
             case SEQ_BINARY: model_name = "GTR2+G"; break;
             case SEQ_MORPH: model_name = "MK+G"; break;
             case SEQ_POMO: model_name = "GTR+P"; break;
             default: ASSERT(0 && "Unprocessed seq_type");
 
         }
+        cout << "Testing " << model_name << " on supermatrix..." << endl;
         concat_tree = testOneModel(model_name, params, conaln, model_info, concat_info,
             models_block, num_threads, BRLEN_OPTIMIZE);
         concat_info.computeICScores(ssize);
@@ -1528,7 +1528,7 @@ void testPartitionModel(Params &params, PhyloSuperTree* in_tree, ModelCheckpoint
         }
         model_info.dump();
 
-        cout << "Single model: " << concat_info.name << " / LnL: " << concat_info.logl
+        cout << concat_info.name << " / LnL: " << concat_info.logl
              << " / df: " << concat_info.df << " / AIC: " << concat_info.AIC_score
              << " / AICc: " << concat_info.AICc_score << " / BIC: " << concat_info.BIC_score << endl;
         delete conaln;
@@ -1613,7 +1613,7 @@ void testPartitionModel(Params &params, PhyloSuperTree* in_tree, ModelCheckpoint
     }
 
 	double inf_score = computeInformationScore(lhsum, dfsum, ssize, params.model_test_criterion);
-	cout << "Full partition model " << criterionName(params.model_test_criterion) << " score: " << inf_score << " (lh=" << lhsum << "  df=" << dfsum << ")" << endl;
+	cout << "Full partition model " << criterionName(params.model_test_criterion) << " score: " << inf_score << " (LnL: " << lhsum << "  df:" << dfsum << ")" << endl;
 
 	if (params.model_name.find("LINK") == string::npos && params.model_name.find("MERGE") == string::npos) {
 		in_tree->printBestPartition((string(params.out_prefix) + ".best_scheme.nex").c_str());
@@ -1789,7 +1789,7 @@ void testPartitionModel(Params &params, PhyloSuperTree* in_tree, ModelCheckpoint
             ASSERT(inf_score <= opt_pair.score + 0.1);
 
             cout << "Merging " << opt_pair.set_name << " with " << criterionName(params.model_test_criterion)
-                 << " score: " << inf_score << " (lh=" << lhsum << "  df=" << dfsum << ")" << endl;
+                 << " score: " << inf_score << " (LnL: " << lhsum << "  df: " << dfsum << ")" << endl;
             // change entry opt_part1 to merged one
             gene_sets[opt_pair.part1] = opt_pair.merged_set;
             lhvec[opt_pair.part1] = opt_pair.logl;
diff --git a/model/modelunrest.cpp b/model/modelunrest.cpp
index 21250450..75078425 100644
--- a/model/modelunrest.cpp
+++ b/model/modelunrest.cpp
@@ -15,7 +15,7 @@ ModelUnrest::ModelUnrest(PhyloTree *tree, string model_params)
 	for (int i=0; i< num_params; i++) model_parameters[i] = 1;
 	setRates();
 	if (model_params != "") {
-		cerr << "WARNING: Supplying model params to constructor not yet properly implemented -- ignored" << endl;
+		cout << "WARNING: Supplying model params to constructor not yet properly implemented -- ignored" << endl;
 		// TODO: parse model_params into model_parameters, then call setRates().
 	}
     name = "UNREST";
diff --git a/tree/phylokernelnew.h b/tree/phylokernelnew.h
index 49e6c40a..20c07ade 100644
--- a/tree/phylokernelnew.h
+++ b/tree/phylokernelnew.h
@@ -2496,7 +2496,7 @@ void PhyloTree::computeLikelihoodDervGenericSIMD(PhyloNeighbor *dad_branch, Phyl
     }
 
     if (std::isnan(*df) || std::isinf(*df)) {
-        cerr << "WARNING: Numerical underflow for lh-derivative" << endl;
+        cout << "WARNING: Numerical underflow for lh-derivative" << endl;
         *df = *ddf = 0.0;
     }
 }
@@ -3398,7 +3398,7 @@ void PhyloTree::computeLikelihoodDervMixlenGenericSIMD(PhyloNeighbor *dad_branch
     }
 
     if (std::isnan(df) || std::isinf(df)) {
-        cerr << "WARNING: Numerical underflow for lh-derivative-mixlen" << endl;
+        cout << "WARNING: Numerical underflow for lh-derivative-mixlen" << endl;
         df = ddf = 0.0;
     }
 }
diff --git a/tree/quartet.cpp b/tree/quartet.cpp
index 14f6fb20..35c5ea31 100644
--- a/tree/quartet.cpp
+++ b/tree/quartet.cpp
@@ -1272,7 +1272,7 @@ void PhyloTree::readLikelihoodMappingGroups(char *filename, QuartetGroups &LMGro
 		for (vector<string>::iterator it = (*i)->taxlist.begin(); it != (*i)->taxlist.end(); it++) {
 			taxid = aln->getSeqID(*it);
 			if (taxid < 0) {
-				cout << "Warning: unknown sequence name \"" << (*it) << "\"! Will be ignored." << endl;
+				cout << "WARNING: unknown sequence name \"" << (*it) << "\"! Will be ignored." << endl;
 			} else {
 				LMGroups.GroupX[t] = taxid;
 				// cout << "  " << (*it) << " (" << taxid << "," << LMGroups.GroupX[t] << ")" << endl;
@@ -1281,7 +1281,7 @@ void PhyloTree::readLikelihoodMappingGroups(char *filename, QuartetGroups &LMGro
 			}
 		}
 		if (numtax != t) {
-			cout << "Warning: ignored cluster did contain unknown sequence names!" << endl;
+			cout << "WARNING: ignored cluster did contain unknown sequence names!" << endl;
 			LMGroups.numGrpSeqs[4] = t;
 		}
 	} else {
@@ -1309,7 +1309,7 @@ void PhyloTree::readLikelihoodMappingGroups(char *filename, QuartetGroups &LMGro
 		for (vector<string>::iterator it = (*i)->taxlist.begin(); it != (*i)->taxlist.end(); it++) {
 			taxid = aln->getSeqID(*it);
 			if (taxid < 0) {
-				cout << "Warning: sequence name \"" << (*it) << "\"! Will be ignored." << endl;
+				cout << "WARNING: sequence name \"" << (*it) << "\"! Will be ignored." << endl;
 			} else {
 				switch(n){
 					case 0: LMGroups.GroupA[t] = taxid;