diff --git a/CMakeLists.txt b/CMakeLists.txt
index ca5ebac72..2f7eb503a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -87,7 +87,7 @@ endif()
 # The version number.
 set (iqtree_VERSION_MAJOR 2)
 set (iqtree_VERSION_MINOR 3)
-set (iqtree_VERSION_PATCH ".5")
+set (iqtree_VERSION_PATCH ".6")
 
 option(BUILD_SHARED_LIBS "Build Shared Libraries" OFF)
 
diff --git a/main/phyloanalysis.cpp b/main/phyloanalysis.cpp
index e712707bc..ac71027f4 100644
--- a/main/phyloanalysis.cpp
+++ b/main/phyloanalysis.cpp
@@ -323,7 +323,7 @@ void reportNexusFile(ostream &out, ModelSubst *m) {
     double f = 1.0 / m->num_states;
     for (i = 0; i < m->num_states; i++)
         out << " " << f;
-    out << endl;
+    out << ";" << endl;
     out.precision(4);
     out << "end;" << endl;
 }
diff --git a/model/modelmixture.cpp b/model/modelmixture.cpp
index 5a7008a35..de8772e39 100644
--- a/model/modelmixture.cpp
+++ b/model/modelmixture.cpp
@@ -2429,8 +2429,8 @@ void ModelMixture::setBounds(double *lower_bound, double *upper_bound, bool *bou
         // only consider the first class as this is a linked substitution matrix
         iterator it = begin();
         auto freq = (*it)->freq_type;
-        int ndim = (*it)->getNDim();
         (*it)->freq_type=FREQ_USER_DEFINED;
+        int ndim = (*it)->getNDim();
         (*it)->setBounds(&lower_bound[dim], &upper_bound[dim], &bound_check[dim]);
         (*it)->freq_type=freq;
         //manually set these params for the restartParameters method; TODO: properly fix this -JD
diff --git a/model/modelprotein.cpp b/model/modelprotein.cpp
index 4e5d7196e..4359c5446 100644
--- a/model/modelprotein.cpp
+++ b/model/modelprotein.cpp
@@ -995,7 +995,9 @@ void ModelProtein::init(const char *model_name, string model_params, StateFreqTy
         } else {
             // initialize rate matrix with a model (default: POISSON) -JD
             nxs_model = models_block->findModel(Params::getInstance().gtr20_model);
-            ASSERT(nxs_model);
+            if (nxs_model == nullptr) {
+                outError("Unknown init model: " + Params::getInstance().gtr20_model);
+            }
             readParametersString(nxs_model->description, false);
             rescaleRates(rates, getNumRateEntries());
         }
diff --git a/tree/phylosupertree.cpp b/tree/phylosupertree.cpp
index 21fabf81d..dcde7a0ed 100644
--- a/tree/phylosupertree.cpp
+++ b/tree/phylosupertree.cpp
@@ -1535,9 +1535,12 @@ void PhyloSuperTree::printBestPartitionParams(const char *filename) {
             if (!saln->partitions[part]->aln_file.empty()) out << saln->partitions[part]->aln_file << ": ";
             /*if (saln->partitions[part]->seq_type == SEQ_CODON)
                 out << "CODON, ";*/
-            out << saln->partitions[part]->sequence_type << ", ";
+            out << saln->partitions[part]->sequence_type;
             string pos = saln->partitions[part]->position_spec;
             replace(pos.begin(), pos.end(), ',' , ' ');
+            if (!saln->partitions[part]->sequence_type.empty() && !pos.empty()) {
+                out << ", ";
+            }
             out << pos << ";" << endl;
         }
         out << "  charpartition mymodels =" << endl;
diff --git a/utils/tools.cpp b/utils/tools.cpp
index 10930e466..a7e91dc2f 100644
--- a/utils/tools.cpp
+++ b/utils/tools.cpp
@@ -1689,8 +1689,9 @@ void parseArg(int argc, char *argv[], Params &params) {
             if (strcmp(argv[cnt], "--gtr20-model") == 0 || strcmp(argv[cnt], "--init-exchange") == 0) {
                 cnt++;
                 if (cnt >= argc)
-                    throw "Use --gtr20-model <POISSON/LG>";
+                    throw "Use " + string(argv[cnt-1]) + " <protein model name>";
                 params.gtr20_model = argv[cnt];
+                transform(params.gtr20_model.begin(), params.gtr20_model.end(), params.gtr20_model.begin(), ::toupper);
                 continue;
             }
             if (strcmp(argv[cnt], "--guess-multiplier") == 0) {