diff --git a/pages/methods.vue b/pages/methods.vue
index 55a3d1d..ef3f07d 100644
--- a/pages/methods.vue
+++ b/pages/methods.vue
@@ -21,6 +21,20 @@
         databases.
       </template>
 
+      <template #multiple-sequence-alignment>
+        Bacterial and archaeal multiple sequence alignments (MSAs) are formed from the concatenation of 120 (bac120)
+        or 53 (arc53) phylogenetically informative markers, respectively. These markers are comprised of
+        proteins or protein domains specified in the Pfam v33.1 or TIGRFAMs v15.0 databases. Details on
+        these markers are available for download (<a href="https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/" target="_blank">here</a>). Gene calling is performed with Prodigal v2.6.3,
+        and markers identified and aligned using HMMER v3.1b1. Columns in the MSA with >50% gaps or with a
+        single amino acid spanning <25% or >95% of taxa are removed. In order to reduce computational
+        requirements of the bacterial reference tree, 42 amino acids per marker were randomly selected
+        from the remaining columns to produce a MSA of ~5,000 columns. The final masks applied to the
+        concatenated MSAs are available for download (<a href="https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/" target="_blank">here</a>)
+        and the identical filtering approach is implemented in <a href="https://github.com/ecogenomics/gtdbtk" target="_blank">GTDB-Tk</a>.
+      </template>
+
+
       <template #tree-inference>
         <p>
 
@@ -322,6 +336,7 @@ export default Vue.extend({
   data: () => ({
     items: [
       {text: 'Gene identification', ref: 'gene-identification'},
+      {text: 'Multiple sequence alignment', ref: 'multiple-sequence-alignment'},
       {text: 'Tree inference', ref: 'tree-inference'},
       {text: 'Identifying 16S rRNA sequences', ref: 'identifying-16s-rrna-sequences'},
       {text: 'Average nucleotide identity', ref: 'average-nucleotide-identity'},
diff --git a/pages/tree.vue b/pages/tree.vue
index a30823b..05ace4e 100644
--- a/pages/tree.vue
+++ b/pages/tree.vue
@@ -34,6 +34,34 @@
         <TreeLegend
           class="pa-2 mt-5"
         />
+
+        <!-- Annotations selection options -->
+        <div class="treeAnnotation rounded-lg mt-5 pa-2" style="font-size: 12px;">
+          <v-row no-gutters>
+            <b>Counts</b>
+          </v-row>
+          <v-row no-gutters>
+            <v-checkbox
+              dense
+              v-model="showDescGenomes"
+              class="font-12px"
+              label="Genomes"
+              hide-details
+            ></v-checkbox>
+          </v-row>
+          <v-row no-gutters>
+            <v-checkbox
+              dense
+              color="#9e94ca"
+              v-model="showDescChildren"
+              class="font-12px"
+              label="Children"
+              hide-details
+            ></v-checkbox>
+            <TreePopUpHelp class="ml-3 my-auto"></TreePopUpHelp>
+          </v-row>
+        </div>
+
       </div>
     </v-navigation-drawer>
 
@@ -125,7 +153,7 @@
                       </v-chip>
 
                       <!-- Add the taxon count -->
-                      <v-chip v-if="showDescChildren && item.nDescChildren" x-small color="#9e94ca" class="m-2">
+                      <v-chip v-if="showDescChildren && item.nDescChildren" x-small color="#9e94ca" class="m-2 chip-white">
                         {{ item.nDescChildren.toLocaleString() }}
                       </v-chip>
 
@@ -546,4 +574,8 @@ export default Vue.extend({
 .font-12px .v-label {
   font-size: 13px !important;
 }
+
+/*.chip-white .v-chip__content {*/
+/*  color: white;*/
+/*}*/
 </style>