diff --git a/app/models/fel.js b/app/models/fel.js
index c4933642..9ec1e38a 100644
--- a/app/models/fel.js
+++ b/app/models/fel.js
@@ -15,6 +15,16 @@ var FEL = mongoose.Schema({
   resample: Number,
   ci: Boolean,
   bootstrap: Boolean,
+  multiple_hits: {
+    type: String,
+    enum: ["None", "Double", "Double+Triple"],
+    default: "None",
+  },
+  site_multihit: {
+    type: String,
+    enum: ["Estimate", "Global"],
+    default: "Estimate",
+  },
 });
 
 FEL.add(AnalysisSchema);
@@ -47,7 +57,7 @@ FEL.virtual("original_fn").get(function () {
       "/../../uploads/msa/" +
       this._id +
       "-original." +
-      this.original_extension
+      this.original_extension,
   );
 });
 
@@ -123,7 +133,7 @@ FEL.statics.spawn = function (fn, options, callback) {
         } else {
           var move = Msa.removeTreeFromFile(
             fel_result.filepath,
-            fel_result.filepath
+            fel_result.filepath,
           );
           move.then(
             (val) => {
@@ -137,7 +147,7 @@ FEL.statics.spawn = function (fn, options, callback) {
             },
             (reason) => {
               callback(err, "issue removing tree from file");
-            }
+            },
           );
         }
       }
diff --git a/app/routes/fel.js b/app/routes/fel.js
index cdd89c3f..711919f7 100644
--- a/app/routes/fel.js
+++ b/app/routes/fel.js
@@ -36,6 +36,8 @@ exports.uploadFile = function (req, res) {
   fel.original_extension = path.basename(fn).split(".")[1];
   fel.mail = postdata.mail;
   fel.ci = postdata.confidence_interval == "true";
+  fel.multiple_hits = postdata.multiple_hits;
+  fel.site_multihit = postdata.site_multihit;
 
   // Check advanced options
   if (!_.isNaN(resample)) {
@@ -87,7 +89,7 @@ exports.uploadFile = function (req, res) {
         } else {
           var move = Msa.removeTreeFromFile(
             fel_result.filepath,
-            fel_result.filepath
+            fel_result.filepath,
           );
           move.then(
             (val) => {
@@ -98,7 +100,7 @@ exports.uploadFile = function (req, res) {
             },
             (reason) => {
               res.json(500, { error: "issue removing tree from file" });
-            }
+            },
           );
         }
       }
@@ -116,7 +118,7 @@ exports.uploadFile = function (req, res) {
           helpers.moveSafely(
             req.files.files.file,
             fel_result.filepath,
-            move_cb
+            move_cb,
           );
         });
       });
@@ -148,6 +150,8 @@ exports.invoke = function (req, res) {
     // User Parameters
     fel.tagged_nwk_tree = postdata.nwk_tree;
     fel.analysis_type = postdata.analysis_type;
+    fel.multiple_hits = postdata.multiple_hits; // new
+    fel.site_multihit = postdata.site_multihit; // new
     fel.status = fel.status_stack[0];
 
     fel.save(function (err, result) {
diff --git a/app/templates/fel/msa_form.ejs b/app/templates/fel/msa_form.ejs
index 550d3e37..8d5eacac 100644
--- a/app/templates/fel/msa_form.ejs
+++ b/app/templates/fel/msa_form.ejs
@@ -88,6 +88,22 @@
         </select>
       </div>
 
+      <div class="form-group">
+        <label for="multiple-hits">Multiple Hits</label>
+        <select name="multiple_hits" id="multiple-hits">
+          <option value="None">None (Single mutations only)</option>
+          <option value="Double">Double (Branch-specific rates for double substitutions)</option>
+          <option value="Double+Triple">Double+Triple (Branch-specific rates for double and triple substitutions)</option>
+        </select>
+      </div>
+
+      <div class="form-group">
+        <label for="estimated-rates">Site Multihit</label>
+        <select name="site_multihit" id="site-multihit">
+          <option value="Estimate">Estimate (Branch-specific rates for substitutions based on model fit)</option>
+          <option value="Global">Global (Rates derived from global model fit)</option>
+        </select>
+      </div>
 
       <div class="form-group <%if (typeof errors != "undefined" && typeof errors.mail != "undefined") { %>has-error<% } %>">
         <label id="datatype-content" class="control-label">Notify When Completed?</label>
diff --git a/public/assets/js/fel/msa_form.js b/public/assets/js/fel/msa_form.js
index c19ec83c..593bc1ac 100644
--- a/public/assets/js/fel/msa_form.js
+++ b/public/assets/js/fel/msa_form.js
@@ -13,17 +13,19 @@ $(function () {
     formData.append("gencodeid", $("select[name='gencodeid']").val());
     formData.append("ds_variation", $("#ds-variation").val());
     formData.append("resample", $("#resample").val());
+    formData.append("multiple_hits", $("select[name='multiple_hits']").val());
+    formData.append("site_multihit", $("select[name='site_multihit']").val());
 
     formData.append(
       "receive_mail",
-      $("input[name='receive_mail']").prop("checked")
+      $("input[name='receive_mail']").prop("checked"),
     );
 
     formData.append("mail", $("input[name='mail']").val());
 
     formData.append(
       "confidence_interval",
-      $("input[name='confidence-interval']").prop("checked")
+      $("input[name='confidence-interval']").prop("checked"),
     );
 
     var action_url = $("#msa-form").attr("action");
@@ -64,7 +66,7 @@ $(function () {
         window.location.href = result.upload_redirect_path;
       } else {
         $("#modal-error-msg").text(
-          "We received data in an unexpected format from the server."
+          "We received data in an unexpected format from the server.",
         );
         $("#errorModal").modal();
         $("#file-progress").css("display", "none");