diff --git a/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java b/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java
index 14f58925db2f77fb45faa1ea979e6ef4f0b03448..19cb69582b3c270bb6529aa7686c5f34473b6466 100644
--- a/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java
@@ -2091,10 +2091,6 @@ public class Phylogeny {
             check_if_single_copy_groups = true;
         }
         single_copy_input_file = SELECTED_HMGROUPS;
-        report_number_of_threads(true, true); // prints how many threads were selected by user
-        if (PHENOTYPE == null) {
-            System.out.println("No --phenotype was provided, tree will only contain genome numbers");
-        }
        
         try (Transaction tx = graphDb.beginTx()) { // start database transaction
             Node pangenome_node = graphDb.findNodes(pangenome_label).next();
@@ -2116,7 +2112,7 @@ public class Phylogeny {
         MultipleSequenceAlignment msa = new MultipleSequenceAlignment(
                 msaMethod,
                 false,
-                false,
+                true,
                 true
         );
         System.out.println();
@@ -2461,7 +2457,7 @@ public class Phylogeny {
         MultipleSequenceAlignment msa = new MultipleSequenceAlignment(
                 "per_group",
                 false,
-                false,
+                true,
                 false
         );
         msa.alignSequences(true, false);
@@ -2808,12 +2804,12 @@ public class Phylogeny {
      */
     public String check_mode_for_snp_tree() {
         String alignment_phylogeny_mode = "";
-        if (Mode.equals("0")) { // no --mode was provided
+        if (Mode.equals("0")) { // no --clustering-method was provided
            if (PROTEOME) {
-               System.out.println("\rNo --mode selected. Preparing Maximum Likelihood phylogeny for protein sequences");
+               System.out.println("\rNo --clustering-method selected. Preparing Maximum Likelihood phylogeny for protein sequences");
                alignment_phylogeny_mode = "ML,protein";
            } else { // pangenome
-               System.out.println("\rNo --mode selected. Preparing Maximum Likelihood phylogeny for nucleotide sequences");
+               System.out.println("\rNo --clustering-method selected. Preparing Maximum Likelihood phylogeny for nucleotide sequences");
                alignment_phylogeny_mode = "ML,nucleotide";
            }
         } else if (CLUSTERING_METHOD.equals("NJ")) {
@@ -2833,7 +2829,7 @@ public class Phylogeny {
                 alignment_phylogeny_mode = "ML,nucleotide";
             }
         } else {
-           System.out.println("\rThe provided --mode argument is not recognized");
+           System.out.println("\rThe provided --clustering-method argument is not recognized");
            System.exit(1);
         }