diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index cc478c4..d8b90e2 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,2 +1,3 @@
 id,fasta,reference,optional_data
-seatoxin-ref,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz
\ No newline at end of file
+seatoxin-ref,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz
+toxin-ref,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/toxin-ref.fa,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/toxin.ref,
\ No newline at end of file
diff --git a/assets/toolsheet.csv b/assets/toolsheet.csv
index a5f1b6e..2ae1536 100644
--- a/assets/toolsheet.csv
+++ b/assets/toolsheet.csv
@@ -1,3 +1,4 @@
 tree,args_tree,aligner,args_aligner
 ,,FOLDMASON,
-FAMSA,,FAMSA,
\ No newline at end of file
+FAMSA,,FAMSA,
+FAMSA,,FOLDMASON,
\ No newline at end of file
diff --git a/bin/shiny_app/shiny_app.py b/bin/shiny_app/shiny_app.py
index 77c395e..dd79529 100644
--- a/bin/shiny_app/shiny_app.py
+++ b/bin/shiny_app/shiny_app.py
@@ -30,9 +30,9 @@
     sys.exit(1)
 
 def merge_tree_args(row):
-    if str(row["tree"]) == "nan":
+    if str(row["tree"]) == "DEFAULT":
         return "None"
-    elif str(row["args_tree"]) == "nan":
+    elif str(row["args_tree"]) == "default":
         return str(row["tree"]) + " ()"
     else:
         return str(row["tree"]) + " (" + str(row["args_tree"]) + ")"
@@ -42,7 +42,7 @@ def merge_tree_args(row):
 def merge_aligner_args(row):
     if str(row["aligner"]) == "nan":
         return "None"
-    elif str(row["args_aligner"]) == "nan":
+    elif str(row["args_aligner"]) == "default":
         return str(row["aligner"]) + " ()"
     else:
         return str(row["aligner"]) + " (" + str(row["args_aligner"]) + ")"
diff --git a/conf/modules.config b/conf/modules.config
index 6a7c143..b026fd5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -74,7 +74,7 @@
                     meta.args_tree ? "args: ${meta.args_tree}" : ""
                 ].join(' ').trim()
             }
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}" }
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}" }
             ext.args = { "${meta.args_tree}" == "null" ? '' : "${meta.args_tree}" }
             publishDir = [
                 path: { "${params.outdir}/trees/${meta.id}" },
@@ -99,7 +99,7 @@
                     meta.args_aligner ? "args: ${meta.args_aligner}" : ""
                 ].join(' ').trim()
             }
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
             ext.args = { "${meta.args_aligner}" == "null" ? '' : "${meta.args_aligner}" }
             if(params.skip_compression){
                 publishDir = [
@@ -119,7 +119,7 @@
                     meta.args_aligner ? "args: ${meta.args_aligner}" : ""
                 ].join(' ').trim()
             }
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
             ext.args = { "${meta.args_aligner}" == "null" ? '' : "${meta.args_aligner}" }
             if(params.skip_compression){
                 publishDir = [
@@ -174,21 +174,21 @@
         //
 
         withName: 'PARSE_IRMSD' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_irmsd" }
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_irmsd" }
         }
 
         withName: 'TCOFFEE_ALNCOMPARE_SP' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_sp" }
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_sp" }
             ext.args = "-compare_mode sp"
         }
 
         withName: 'TCOFFEE_ALNCOMPARE_TC' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_tc" }
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_tc" }
             ext.args = "-compare_mode tc"
         }
 
         withName: 'TCOFFEE_IRMSD' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_irmsd" }
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_irmsd" }
             publishDir = [
                 path: { "${params.outdir}/evaluation/${task.process.tokenize(':')[-1].toLowerCase()}" },
                 mode: params.publish_dir_mode,
@@ -198,7 +198,7 @@
         }
 
         withName: "CALC_GAPS" {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_gaps" }
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_gaps" }
         }
 
         withName: "CONCAT_IRMSD" {
@@ -222,7 +222,7 @@
         }
 
         withName: 'TCOFFEE_TCS' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_tcs" }
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}_tcs" }
             publishDir = [
                 path: { "${params.outdir}/evaluation/${task.process.tokenize(':')[-1].toLowerCase()}" },
                 mode: params.publish_dir_mode,
@@ -274,7 +274,7 @@
         // Visualization
         //
         withName: 'FOLDMASON_MSA2LDDTREPORT' {
-            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
+            ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.args_tree_clean}_${meta.aligner}-args-${meta.args_aligner_clean}" }
             publishDir = [
                 path: { "${params.outdir}/visualization" },
                 mode: params.publish_dir_mode,
diff --git a/subworkflows/local/align.nf b/subworkflows/local/align.nf
index 59538c5..c852061 100644
--- a/subworkflows/local/align.nf
+++ b/subworkflows/local/align.nf
@@ -49,6 +49,7 @@ workflow ALIGN {
         }
         .set { ch_tools_split }
 
+    ch_tools.view()
     // ------------------------------------------------
     // Compute the required trees
     // ------------------------------------------------
diff --git a/subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf b/subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf
index 12af446..4c41253 100644
--- a/subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf
@@ -357,12 +357,21 @@ class Utils {
         // if clearnArgs is empty, return ""
 
         if (cleanArgs == null || cleanArgs == "") {
-            return ""
+            return "default"
         }else{
             return cleanArgs
         }
     }
 
+    public static clean_tree(argsTree){
+
+        def tree = argsTree.toString()
+        if(tree == null || tree == "" || tree == "null"){
+            return "DEFAULT"
+        }
+        return tree
+    }
+
     public static fix_args(tool,args,tool_to_be_checked, required_flag, default_value) {
         /*
         This function checks if the required_flag is present in the args string for the tool_to_be_checked.
diff --git a/subworkflows/local/visualization.nf b/subworkflows/local/visualization.nf
index 037a4e1..c228165 100644
--- a/subworkflows/local/visualization.nf
+++ b/subworkflows/local/visualization.nf
@@ -13,6 +13,8 @@ workflow VISUALIZATION {
     ch_versions     = Channel.empty()
     ch_html         = Channel.empty()
 
+
+    ch_msa.view()
     // Merge the msa and tree 
     // split the msa meta to be able to merge with the tree meta
     ch_msa