diff --git a/public/js/form.js b/public/js/form.js
index 3ceea51f9..95e35aa9a 100644
--- a/public/js/form.js
+++ b/public/js/form.js
@@ -156,16 +156,17 @@ export class Form extends Component {
     }
 
     handleAlgoChanged(algo) {
-        if (this.state.preDefinedOpts.hasOwnProperty(algo)) {
+        if (algo in this.state.preDefinedOpts) {
             var preDefinedOpts = this.state.preDefinedOpts[algo];
             this.refs.opts.setState({
+                method: algo,
                 preOpts: preDefinedOpts,
                 value: (preDefinedOpts['last search'] ||
                     preDefinedOpts['default']).join(' ')
             });
         }
         else {
-            this.refs.opts.setState({ preOpts: {}, value: '' });
+            this.refs.opts.setState({ preOpts: {}, value: '', method: '' });
         }
     }
 
diff --git a/public/js/options.js b/public/js/options.js
index d18b62eb9..c78f2cb17 100644
--- a/public/js/options.js
+++ b/public/js/options.js
@@ -3,9 +3,10 @@ import React, { Component } from 'react';
 export class Options extends Component {
     constructor(props) {
         super(props);
-        this.state = { preOpts: {}, value: '' };
+        this.state = { preOpts: {}, value: '', method: '' };
         this.updateBox = this.updateBox.bind(this);
         this.optionsJSX = this.optionsJSX.bind(this);
+        this.showAdvancedOptions = this.showAdvancedOptions.bind(this);
     }
 
     updateBox(value) {
@@ -37,7 +38,14 @@ export class Options extends Component {
             </ul>
         </span>;
     }
-
+    showAdvancedOptions(e) {
+        const ids = ['blastn', 'tblastn', 'blastp', 'blastx', 'tblastx'];
+        const method = this.state.method.toLowerCase();
+        // hide options for other algorithms and only show for selected algorithm
+        for (const id of ids) {
+            $(`#${id}`)[id === method ? 'show' : 'hide']();
+        }
+    }
     render() {
         var classNames = 'form-control';
         if (this.state.value.trim()) {
@@ -50,12 +58,14 @@ export class Options extends Component {
                         <div className="input-group">
                             <label className="control-label" htmlFor="advanced">
                                 Advanced parameters:
-                                <sup style={{ marginLeft: '2px' }}>
+                                {/* only show link to advanced parameters if blast method is known */}
+                                {this.state.method && <sup style={{ marginLeft: '2px' }}>
                                     <a href=''
+                                        onClick={this.showAdvancedOptions}
                                         data-toggle="modal" data-target="#help">
                                         <i className="fa fa-question-circle"></i>
                                     </a>
-                                </sup>
+                                </sup>}
                             </label>
                             <input type="text" className={classNames}
                                 onChange={e => this.updateBox(e.target.value)}
diff --git a/public/sequenceserver-search.min.js b/public/sequenceserver-search.min.js
index 8d6f874e2..7b2efa11b 100644
--- a/public/sequenceserver-search.min.js
+++ b/public/sequenceserver-search.min.js
@@ -60,7 +60,7 @@ eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpac
 /***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
 
 "use strict";
-eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */   \"Form\": () => (/* binding */ Form)\n/* harmony export */ });\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! react */ \"./node_modules/react/index.js\");\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(react__WEBPACK_IMPORTED_MODULE_0__);\n/* harmony import */ var _search_button__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! ./search_button */ \"./public/js/search_button.js\");\n/* harmony import */ var _query__WEBPACK_IMPORTED_MODULE_2__ = __webpack_require__(/*! ./query */ \"./public/js/query.js\");\n/* harmony import */ var _databases_tree__WEBPACK_IMPORTED_MODULE_3__ = __webpack_require__(/*! ./databases_tree */ \"./public/js/databases_tree.js\");\n/* harmony import */ var _databases__WEBPACK_IMPORTED_MODULE_4__ = __webpack_require__(/*! ./databases */ \"./public/js/databases.js\");\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_5__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n/* harmony import */ var _options__WEBPACK_IMPORTED_MODULE_6__ = __webpack_require__(/*! ./options */ \"./public/js/options.js\");\n/* harmony import */ var react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__ = __webpack_require__(/*! react/jsx-runtime */ \"./node_modules/react/jsx-runtime.js\");\n/* provided dependency */ var $ = __webpack_require__(/*! jquery */ \"./node_modules/jquery/dist/jquery.js\");\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; return _typeof = \"function\" == typeof Symbol && \"symbol\" == typeof Symbol.iterator ? function (obj) { return typeof obj; } : function (obj) { return obj && \"function\" == typeof Symbol && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }, _typeof(obj); }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, \"prototype\", { writable: false }); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); Object.defineProperty(subClass, \"prototype\", { writable: false }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } else if (call !== void 0) { throw new TypeError(\"Derived constructors may only return object or undefined\"); } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n\n\n\n\n\n\n\n/**\n * Search form.\n *\n * Top level component that initialises and holds all other components, and\n * facilitates communication between them.\n */\n\n\n\nvar Form = /*#__PURE__*/function (_Component) {\n  _inherits(Form, _Component);\n\n  var _super = _createSuper(Form);\n\n  function Form(props) {\n    var _this;\n\n    _classCallCheck(this, Form);\n\n    _this = _super.call(this, props);\n    _this.state = {\n      databases: [],\n      preDefinedOpts: {},\n      tree: {}\n    };\n    _this.useTreeWidget = _this.useTreeWidget.bind(_assertThisInitialized(_this));\n    _this.determineBlastMethod = _this.determineBlastMethod.bind(_assertThisInitialized(_this));\n    _this.handleSequenceTypeChanged = _this.handleSequenceTypeChanged.bind(_assertThisInitialized(_this));\n    _this.handleDatabaseTypeChanaged = _this.handleDatabaseTypeChanaged.bind(_assertThisInitialized(_this));\n    _this.handleAlgoChanged = _this.handleAlgoChanged.bind(_assertThisInitialized(_this));\n    _this.handleFormSubmission = _this.handleFormSubmission.bind(_assertThisInitialized(_this));\n    _this.formRef = /*#__PURE__*/(0,react__WEBPACK_IMPORTED_MODULE_0__.createRef)();\n    return _this;\n  }\n\n  _createClass(Form, [{\n    key: \"componentDidMount\",\n    value: function componentDidMount() {\n      /** \n      * Fetch data to initialise the search interface from the server. These\n      * include list of databases to search against, advanced options to\n      * apply when an algorithm is selected, and a query sequence that\n      * the user may want to search in the databases.\n      */\n      var search = location.search.split(/\\?|&/).filter(Boolean);\n      var job_id = sessionStorage.getItem('job_id');\n\n      if (job_id) {\n        search.unshift(\"job_id=\".concat(job_id));\n      }\n\n      $.getJSON(\"searchdata.json?\".concat(search.join('&')), function (data) {\n        /* Update form state (i.e., list of databases and predefined\n         * advanced options.\n         */\n        this.setState({\n          tree: data['tree'],\n          databases: data['database'],\n          preSelectedDbs: data['preSelectedDbs'],\n          preDefinedOpts: data['options']\n        });\n        /* Pre-populate the form with server sent query sequences\n         * (if any).\n         */\n\n        if (data['query']) {\n          this.refs.query.value(data['query']);\n        }\n\n        setTimeout(function () {\n          $('.jstree_div').click();\n        }, 1000);\n      }.bind(this));\n      /* Enable submitting form on Cmd+Enter */\n\n      $(document).on('keydown', function (e) {\n        var $button = $('#method');\n\n        if (!$button.is(':disabled') && e.ctrlKey && e.key === 'Enter') {\n          $button.trigger('click');\n        }\n      }); // show overlay to create visual feedback on button click \n\n      $('#method').on('click', function () {\n        $('#overlay').css('display', 'block');\n      });\n    }\n  }, {\n    key: \"useTreeWidget\",\n    value: function useTreeWidget() {\n      return !underscore__WEBPACK_IMPORTED_MODULE_5__[\"default\"].isEmpty(this.state.tree);\n    }\n  }, {\n    key: \"handleFormSubmission\",\n    value: function handleFormSubmission(evt) {\n      evt.preventDefault();\n      var form = this.formRef.current;\n      var formData = new FormData(form);\n      formData.append('method', this.refs.button.state.methods[0]);\n      fetch(window.location.href, {\n        method: 'POST',\n        body: formData\n      }).then(function (res) {\n        //remove overlay when form is submitted\n        $('#overlay').css('display', 'none'); // redirect\n\n        if (res.redirected && res.url) {\n          // setTimeout is needed here as a workaround because safari doesnt allow async calling of window.open\n          // so setTimeout makes the method get called on the main thread.\n          setTimeout(function () {\n            window.open(res.url, $('#toggleNewTab').is(':checked') ? '_blank' : '_self');\n          }, 0);\n        }\n      });\n    }\n  }, {\n    key: \"determineBlastMethod\",\n    value: function determineBlastMethod() {\n      var database_type = this.databaseType;\n      var sequence_type = this.sequenceType;\n\n      if (this.refs.query.isEmpty()) {\n        return [];\n      } //database type is always known\n\n\n      switch (database_type) {\n        case 'protein':\n          switch (sequence_type) {\n            case undefined:\n              return ['blastp', 'blastx'];\n\n            case 'protein':\n              return ['blastp'];\n\n            case 'nucleotide':\n              return ['blastx'];\n          }\n\n          break;\n\n        case 'nucleotide':\n          switch (sequence_type) {\n            case undefined:\n              return ['tblastn', 'blastn', 'tblastx'];\n\n            case 'protein':\n              return ['tblastn'];\n\n            case 'nucleotide':\n              return ['blastn', 'tblastx'];\n          }\n\n          break;\n      }\n\n      return [];\n    }\n  }, {\n    key: \"handleSequenceTypeChanged\",\n    value: function handleSequenceTypeChanged(type) {\n      this.sequenceType = type;\n      this.refs.button.setState({\n        hasQuery: !this.refs.query.isEmpty(),\n        hasDatabases: !!this.databaseType,\n        methods: this.determineBlastMethod()\n      });\n    }\n  }, {\n    key: \"handleDatabaseTypeChanaged\",\n    value: function handleDatabaseTypeChanaged(type) {\n      this.databaseType = type;\n      this.refs.button.setState({\n        hasQuery: !this.refs.query.isEmpty(),\n        hasDatabases: !!this.databaseType,\n        methods: this.determineBlastMethod()\n      });\n    }\n  }, {\n    key: \"handleAlgoChanged\",\n    value: function handleAlgoChanged(algo) {\n      if (this.state.preDefinedOpts.hasOwnProperty(algo)) {\n        var preDefinedOpts = this.state.preDefinedOpts[algo];\n        this.refs.opts.setState({\n          preOpts: preDefinedOpts,\n          value: (preDefinedOpts['last search'] || preDefinedOpts['default']).join(' ')\n        });\n      } else {\n        this.refs.opts.setState({\n          preOpts: {},\n          value: ''\n        });\n      }\n    }\n  }, {\n    key: \"render\",\n    value: function render() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsxs)(\"div\", {\n        className: \"container\",\n        children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n          id: \"overlay\",\n          style: {\n            position: 'absolute',\n            top: 0,\n            left: 0,\n            width: '100vw',\n            height: '100vw',\n            background: 'rgba(0, 0, 0, 0.2)',\n            display: 'none',\n            zIndex: 99\n          }\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsxs)(\"form\", {\n          id: \"blast\",\n          ref: this.formRef,\n          onSubmit: this.handleFormSubmission,\n          className: \"form-horizontal\",\n          children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n            className: \"form-group query-container\",\n            children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(_query__WEBPACK_IMPORTED_MODULE_2__.SearchQueryWidget, {\n              ref: \"query\",\n              onSequenceTypeChanged: this.handleSequenceTypeChanged\n            })\n          }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsxs)(\"div\", {\n            className: \"notifications\",\n            id: \"notifications\",\n            children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(NucleotideNotification, {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(ProteinNotification, {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(MixedNotification, {})]\n          }), this.useTreeWidget() ? /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(_databases_tree__WEBPACK_IMPORTED_MODULE_3__[\"default\"], {\n            ref: \"databases\",\n            databases: this.state.databases,\n            tree: this.state.tree,\n            preSelectedDbs: this.state.preSelectedDbs,\n            onDatabaseTypeChanged: this.handleDatabaseTypeChanaged\n          }) : /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(_databases__WEBPACK_IMPORTED_MODULE_4__.Databases, {\n            ref: \"databases\",\n            databases: this.state.databases,\n            preSelectedDbs: this.state.preSelectedDbs,\n            onDatabaseTypeChanged: this.handleDatabaseTypeChanaged\n          }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsxs)(\"div\", {\n            className: \"form-group\",\n            children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(_options__WEBPACK_IMPORTED_MODULE_6__.Options, {\n              ref: \"opts\"\n            }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n              className: \"col-md-2\",\n              children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n                className: \"form-group\",\n                style: {\n                  'textAlign': 'center',\n                  'padding': '7px 0'\n                },\n                children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsxs)(\"label\", {\n                  children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"input\", {\n                    type: \"checkbox\",\n                    id: \"toggleNewTab\"\n                  }), \" Open results in new tab\"]\n                })\n              })\n            }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(_search_button__WEBPACK_IMPORTED_MODULE_1__.SearchButton, {\n              ref: \"button\",\n              onAlgoChanged: this.handleAlgoChanged\n            })]\n          })]\n        })]\n      });\n    }\n  }]);\n\n  return Form;\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\nvar ProteinNotification = /*#__PURE__*/function (_Component2) {\n  _inherits(ProteinNotification, _Component2);\n\n  var _super2 = _createSuper(ProteinNotification);\n\n  function ProteinNotification() {\n    _classCallCheck(this, ProteinNotification);\n\n    return _super2.apply(this, arguments);\n  }\n\n  _createClass(ProteinNotification, [{\n    key: \"render\",\n    value: function render() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n        className: \"notification row\",\n        id: \"protein-sequence-notification\",\n        style: {\n          display: 'none'\n        },\n        children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n          className: \"alert-info col-md-6 col-md-offset-3\",\n          children: \"Detected: amino-acid sequence(s).\"\n        })\n      });\n    }\n  }]);\n\n  return ProteinNotification;\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\nvar NucleotideNotification = /*#__PURE__*/function (_Component3) {\n  _inherits(NucleotideNotification, _Component3);\n\n  var _super3 = _createSuper(NucleotideNotification);\n\n  function NucleotideNotification() {\n    _classCallCheck(this, NucleotideNotification);\n\n    return _super3.apply(this, arguments);\n  }\n\n  _createClass(NucleotideNotification, [{\n    key: \"render\",\n    value: function render() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n        className: \"notification row\",\n        id: \"nucleotide-sequence-notification\",\n        style: {\n          display: 'none'\n        },\n        children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n          className: \"alert-info col-md-6 col-md-offset-3\",\n          children: \"Detected: nucleotide sequence(s).\"\n        })\n      });\n    }\n  }]);\n\n  return NucleotideNotification;\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\nvar MixedNotification = /*#__PURE__*/function (_Component4) {\n  _inherits(MixedNotification, _Component4);\n\n  var _super4 = _createSuper(MixedNotification);\n\n  function MixedNotification() {\n    _classCallCheck(this, MixedNotification);\n\n    return _super4.apply(this, arguments);\n  }\n\n  _createClass(MixedNotification, [{\n    key: \"render\",\n    value: function render() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n        className: \"notification row\",\n        id: \"mixed-sequence-notification\",\n        style: {\n          display: 'none'\n        },\n        children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n          className: \"alert-danger col-md-10 col-md-offset-1\",\n          children: \"Error: mixed nucleotide and amino-acid sequences detected.\"\n        })\n      });\n    }\n  }]);\n\n  return MixedNotification;\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\n//# sourceURL=webpack://SequenceServer/./public/js/form.js?");
+eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */   \"Form\": () => (/* binding */ Form)\n/* harmony export */ });\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! react */ \"./node_modules/react/index.js\");\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(react__WEBPACK_IMPORTED_MODULE_0__);\n/* harmony import */ var _search_button__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! ./search_button */ \"./public/js/search_button.js\");\n/* harmony import */ var _query__WEBPACK_IMPORTED_MODULE_2__ = __webpack_require__(/*! ./query */ \"./public/js/query.js\");\n/* harmony import */ var _databases_tree__WEBPACK_IMPORTED_MODULE_3__ = __webpack_require__(/*! ./databases_tree */ \"./public/js/databases_tree.js\");\n/* harmony import */ var _databases__WEBPACK_IMPORTED_MODULE_4__ = __webpack_require__(/*! ./databases */ \"./public/js/databases.js\");\n/* harmony import */ var underscore__WEBPACK_IMPORTED_MODULE_5__ = __webpack_require__(/*! underscore */ \"./node_modules/underscore/modules/index-all.js\");\n/* harmony import */ var _options__WEBPACK_IMPORTED_MODULE_6__ = __webpack_require__(/*! ./options */ \"./public/js/options.js\");\n/* harmony import */ var react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__ = __webpack_require__(/*! react/jsx-runtime */ \"./node_modules/react/jsx-runtime.js\");\n/* provided dependency */ var $ = __webpack_require__(/*! jquery */ \"./node_modules/jquery/dist/jquery.js\");\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; return _typeof = \"function\" == typeof Symbol && \"symbol\" == typeof Symbol.iterator ? function (obj) { return typeof obj; } : function (obj) { return obj && \"function\" == typeof Symbol && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }, _typeof(obj); }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, \"prototype\", { writable: false }); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); Object.defineProperty(subClass, \"prototype\", { writable: false }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } else if (call !== void 0) { throw new TypeError(\"Derived constructors may only return object or undefined\"); } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n\n\n\n\n\n\n\n/**\n * Search form.\n *\n * Top level component that initialises and holds all other components, and\n * facilitates communication between them.\n */\n\n\n\nvar Form = /*#__PURE__*/function (_Component) {\n  _inherits(Form, _Component);\n\n  var _super = _createSuper(Form);\n\n  function Form(props) {\n    var _this;\n\n    _classCallCheck(this, Form);\n\n    _this = _super.call(this, props);\n    _this.state = {\n      databases: [],\n      preDefinedOpts: {},\n      tree: {}\n    };\n    _this.useTreeWidget = _this.useTreeWidget.bind(_assertThisInitialized(_this));\n    _this.determineBlastMethod = _this.determineBlastMethod.bind(_assertThisInitialized(_this));\n    _this.handleSequenceTypeChanged = _this.handleSequenceTypeChanged.bind(_assertThisInitialized(_this));\n    _this.handleDatabaseTypeChanaged = _this.handleDatabaseTypeChanaged.bind(_assertThisInitialized(_this));\n    _this.handleAlgoChanged = _this.handleAlgoChanged.bind(_assertThisInitialized(_this));\n    _this.handleFormSubmission = _this.handleFormSubmission.bind(_assertThisInitialized(_this));\n    _this.formRef = /*#__PURE__*/(0,react__WEBPACK_IMPORTED_MODULE_0__.createRef)();\n    return _this;\n  }\n\n  _createClass(Form, [{\n    key: \"componentDidMount\",\n    value: function componentDidMount() {\n      /** \n      * Fetch data to initialise the search interface from the server. These\n      * include list of databases to search against, advanced options to\n      * apply when an algorithm is selected, and a query sequence that\n      * the user may want to search in the databases.\n      */\n      var search = location.search.split(/\\?|&/).filter(Boolean);\n      var job_id = sessionStorage.getItem('job_id');\n\n      if (job_id) {\n        search.unshift(\"job_id=\".concat(job_id));\n      }\n\n      $.getJSON(\"searchdata.json?\".concat(search.join('&')), function (data) {\n        /* Update form state (i.e., list of databases and predefined\n         * advanced options.\n         */\n        this.setState({\n          tree: data['tree'],\n          databases: data['database'],\n          preSelectedDbs: data['preSelectedDbs'],\n          preDefinedOpts: data['options']\n        });\n        /* Pre-populate the form with server sent query sequences\n         * (if any).\n         */\n\n        if (data['query']) {\n          this.refs.query.value(data['query']);\n        }\n\n        setTimeout(function () {\n          $('.jstree_div').click();\n        }, 1000);\n      }.bind(this));\n      /* Enable submitting form on Cmd+Enter */\n\n      $(document).on('keydown', function (e) {\n        var $button = $('#method');\n\n        if (!$button.is(':disabled') && e.ctrlKey && e.key === 'Enter') {\n          $button.trigger('click');\n        }\n      }); // show overlay to create visual feedback on button click \n\n      $('#method').on('click', function () {\n        $('#overlay').css('display', 'block');\n      });\n    }\n  }, {\n    key: \"useTreeWidget\",\n    value: function useTreeWidget() {\n      return !underscore__WEBPACK_IMPORTED_MODULE_5__[\"default\"].isEmpty(this.state.tree);\n    }\n  }, {\n    key: \"handleFormSubmission\",\n    value: function handleFormSubmission(evt) {\n      evt.preventDefault();\n      var form = this.formRef.current;\n      var formData = new FormData(form);\n      formData.append('method', this.refs.button.state.methods[0]);\n      fetch(window.location.href, {\n        method: 'POST',\n        body: formData\n      }).then(function (res) {\n        //remove overlay when form is submitted\n        $('#overlay').css('display', 'none'); // redirect\n\n        if (res.redirected && res.url) {\n          // setTimeout is needed here as a workaround because safari doesnt allow async calling of window.open\n          // so setTimeout makes the method get called on the main thread.\n          setTimeout(function () {\n            window.open(res.url, $('#toggleNewTab').is(':checked') ? '_blank' : '_self');\n          }, 0);\n        }\n      });\n    }\n  }, {\n    key: \"determineBlastMethod\",\n    value: function determineBlastMethod() {\n      var database_type = this.databaseType;\n      var sequence_type = this.sequenceType;\n\n      if (this.refs.query.isEmpty()) {\n        return [];\n      } //database type is always known\n\n\n      switch (database_type) {\n        case 'protein':\n          switch (sequence_type) {\n            case undefined:\n              return ['blastp', 'blastx'];\n\n            case 'protein':\n              return ['blastp'];\n\n            case 'nucleotide':\n              return ['blastx'];\n          }\n\n          break;\n\n        case 'nucleotide':\n          switch (sequence_type) {\n            case undefined:\n              return ['tblastn', 'blastn', 'tblastx'];\n\n            case 'protein':\n              return ['tblastn'];\n\n            case 'nucleotide':\n              return ['blastn', 'tblastx'];\n          }\n\n          break;\n      }\n\n      return [];\n    }\n  }, {\n    key: \"handleSequenceTypeChanged\",\n    value: function handleSequenceTypeChanged(type) {\n      this.sequenceType = type;\n      this.refs.button.setState({\n        hasQuery: !this.refs.query.isEmpty(),\n        hasDatabases: !!this.databaseType,\n        methods: this.determineBlastMethod()\n      });\n    }\n  }, {\n    key: \"handleDatabaseTypeChanaged\",\n    value: function handleDatabaseTypeChanaged(type) {\n      this.databaseType = type;\n      this.refs.button.setState({\n        hasQuery: !this.refs.query.isEmpty(),\n        hasDatabases: !!this.databaseType,\n        methods: this.determineBlastMethod()\n      });\n    }\n  }, {\n    key: \"handleAlgoChanged\",\n    value: function handleAlgoChanged(algo) {\n      if (algo in this.state.preDefinedOpts) {\n        var preDefinedOpts = this.state.preDefinedOpts[algo];\n        this.refs.opts.setState({\n          method: algo,\n          preOpts: preDefinedOpts,\n          value: (preDefinedOpts['last search'] || preDefinedOpts['default']).join(' ')\n        });\n      } else {\n        this.refs.opts.setState({\n          preOpts: {},\n          value: '',\n          method: ''\n        });\n      }\n    }\n  }, {\n    key: \"render\",\n    value: function render() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsxs)(\"div\", {\n        className: \"container\",\n        children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n          id: \"overlay\",\n          style: {\n            position: 'absolute',\n            top: 0,\n            left: 0,\n            width: '100vw',\n            height: '100vw',\n            background: 'rgba(0, 0, 0, 0.2)',\n            display: 'none',\n            zIndex: 99\n          }\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsxs)(\"form\", {\n          id: \"blast\",\n          ref: this.formRef,\n          onSubmit: this.handleFormSubmission,\n          className: \"form-horizontal\",\n          children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n            className: \"form-group query-container\",\n            children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(_query__WEBPACK_IMPORTED_MODULE_2__.SearchQueryWidget, {\n              ref: \"query\",\n              onSequenceTypeChanged: this.handleSequenceTypeChanged\n            })\n          }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsxs)(\"div\", {\n            className: \"notifications\",\n            id: \"notifications\",\n            children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(NucleotideNotification, {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(ProteinNotification, {}), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(MixedNotification, {})]\n          }), this.useTreeWidget() ? /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(_databases_tree__WEBPACK_IMPORTED_MODULE_3__[\"default\"], {\n            ref: \"databases\",\n            databases: this.state.databases,\n            tree: this.state.tree,\n            preSelectedDbs: this.state.preSelectedDbs,\n            onDatabaseTypeChanged: this.handleDatabaseTypeChanaged\n          }) : /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(_databases__WEBPACK_IMPORTED_MODULE_4__.Databases, {\n            ref: \"databases\",\n            databases: this.state.databases,\n            preSelectedDbs: this.state.preSelectedDbs,\n            onDatabaseTypeChanged: this.handleDatabaseTypeChanaged\n          }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsxs)(\"div\", {\n            className: \"form-group\",\n            children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(_options__WEBPACK_IMPORTED_MODULE_6__.Options, {\n              ref: \"opts\"\n            }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n              className: \"col-md-2\",\n              children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n                className: \"form-group\",\n                style: {\n                  'textAlign': 'center',\n                  'padding': '7px 0'\n                },\n                children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsxs)(\"label\", {\n                  children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"input\", {\n                    type: \"checkbox\",\n                    id: \"toggleNewTab\"\n                  }), \" Open results in new tab\"]\n                })\n              })\n            }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(_search_button__WEBPACK_IMPORTED_MODULE_1__.SearchButton, {\n              ref: \"button\",\n              onAlgoChanged: this.handleAlgoChanged\n            })]\n          })]\n        })]\n      });\n    }\n  }]);\n\n  return Form;\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\nvar ProteinNotification = /*#__PURE__*/function (_Component2) {\n  _inherits(ProteinNotification, _Component2);\n\n  var _super2 = _createSuper(ProteinNotification);\n\n  function ProteinNotification() {\n    _classCallCheck(this, ProteinNotification);\n\n    return _super2.apply(this, arguments);\n  }\n\n  _createClass(ProteinNotification, [{\n    key: \"render\",\n    value: function render() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n        className: \"notification row\",\n        id: \"protein-sequence-notification\",\n        style: {\n          display: 'none'\n        },\n        children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n          className: \"alert-info col-md-6 col-md-offset-3\",\n          children: \"Detected: amino-acid sequence(s).\"\n        })\n      });\n    }\n  }]);\n\n  return ProteinNotification;\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\nvar NucleotideNotification = /*#__PURE__*/function (_Component3) {\n  _inherits(NucleotideNotification, _Component3);\n\n  var _super3 = _createSuper(NucleotideNotification);\n\n  function NucleotideNotification() {\n    _classCallCheck(this, NucleotideNotification);\n\n    return _super3.apply(this, arguments);\n  }\n\n  _createClass(NucleotideNotification, [{\n    key: \"render\",\n    value: function render() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n        className: \"notification row\",\n        id: \"nucleotide-sequence-notification\",\n        style: {\n          display: 'none'\n        },\n        children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n          className: \"alert-info col-md-6 col-md-offset-3\",\n          children: \"Detected: nucleotide sequence(s).\"\n        })\n      });\n    }\n  }]);\n\n  return NucleotideNotification;\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\nvar MixedNotification = /*#__PURE__*/function (_Component4) {\n  _inherits(MixedNotification, _Component4);\n\n  var _super4 = _createSuper(MixedNotification);\n\n  function MixedNotification() {\n    _classCallCheck(this, MixedNotification);\n\n    return _super4.apply(this, arguments);\n  }\n\n  _createClass(MixedNotification, [{\n    key: \"render\",\n    value: function render() {\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n        className: \"notification row\",\n        id: \"mixed-sequence-notification\",\n        style: {\n          display: 'none'\n        },\n        children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_7__.jsx)(\"div\", {\n          className: \"alert-danger col-md-10 col-md-offset-1\",\n          children: \"Error: mixed nucleotide and amino-acid sequences detected.\"\n        })\n      });\n    }\n  }]);\n\n  return MixedNotification;\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\n//# sourceURL=webpack://SequenceServer/./public/js/form.js?");
 
 /***/ }),
 
@@ -115,7 +115,7 @@ eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpac
 /***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
 
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Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n // Component for the advanced params input field.\n\n\n\nvar Options = /*#__PURE__*/function (_Component) {\n  _inherits(Options, _Component);\n\n  var _super = _createSuper(Options);\n\n  function Options(props) {\n    var _this;\n\n    _classCallCheck(this, Options);\n\n    _this = _super.call(this, props);\n    _this.state = {\n      preOpts: {},\n      value: ''\n    };\n    _this.updateBox = _this.updateBox.bind(_assertThisInitialized(_this));\n    _this.optionsJSX = _this.optionsJSX.bind(_assertThisInitialized(_this));\n    return _this;\n  }\n\n  _createClass(Options, [{\n    key: \"updateBox\",\n    value: function updateBox(value) {\n      this.setState({\n        value: value\n      });\n    }\n  }, {\n    key: \"optionsJSX\",\n    value: function optionsJSX() {\n      var _this2 = this;\n\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsxs)(\"span\", {\n        className: \"input-group-btn dropdown\",\n        children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"button\", {\n          className: \"btn bnt-sm btn-default dropdown-toggle\",\n          \"data-toggle\": \"dropdown\",\n          children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"i\", {\n            className: \"fa fa-caret-down\"\n          })\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"ul\", {\n          id: \"advanced-params-dropdown\",\n          className: \"dropdown-menu dropdown-menu-right\",\n          children: Object.entries(this.state.preOpts).map(function (_ref, index) {\n            var _ref2 = _slicedToArray(_ref, 2),\n                key = _ref2[0],\n                value = _ref2[1];\n\n            value = value.join(' ');\n            if (value.trim() === _this2.state.value.trim()) var className = 'yellow-background';\n            return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsxs)(\"li\", {\n              className: className,\n              onClick: function onClick() {\n                return _this2.updateBox(value);\n              },\n              children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsxs)(\"strong\", {\n                children: [key, \":\"]\n              }), \"\\xA0\", value]\n            }, index);\n          })\n        })]\n      });\n    }\n  }, {\n    key: \"render\",\n    value: function render() {\n      var _this3 = this;\n\n      var classNames = 'form-control';\n\n      if (this.state.value.trim()) {\n        classNames += ' yellow-background';\n      }\n\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"div\", {\n        className: \"col-md-7\",\n        children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"div\", {\n          className: \"form-group\",\n          children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"div\", {\n            className: \"col-md-12\",\n            children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsxs)(\"div\", {\n              className: \"input-group\",\n              children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsxs)(\"label\", {\n                className: \"control-label\",\n                htmlFor: \"advanced\",\n                children: [\"Advanced parameters:\", /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"sup\", {\n                  style: {\n                    marginLeft: '2px'\n                  },\n                  children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"a\", {\n                    href: \"\",\n                    \"data-toggle\": \"modal\",\n                    \"data-target\": \"#help\",\n                    children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"i\", {\n                      className: \"fa fa-question-circle\"\n                    })\n                  })\n                })]\n              }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"input\", {\n                type: \"text\",\n                className: classNames,\n                onChange: function onChange(e) {\n                  return _this3.updateBox(e.target.value);\n                },\n                id: \"advanced\",\n                name: \"advanced\",\n                value: this.state.value,\n                placeholder: \"eg: -evalue 1.0e-5 -num_alignments 100\",\n                title: \"View, and enter advanced parameters.\"\n              }), Object.keys(this.state.preOpts).length > 1 && this.optionsJSX()]\n            })\n          })\n        })\n      });\n    }\n  }]);\n\n  return Options;\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\n//# sourceURL=webpack://SequenceServer/./public/js/options.js?");
+eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */   \"Options\": () => (/* binding */ Options)\n/* harmony export */ });\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! react */ \"./node_modules/react/index.js\");\n/* harmony import */ var react__WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(react__WEBPACK_IMPORTED_MODULE_0__);\n/* harmony import */ var react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! react/jsx-runtime */ \"./node_modules/react/jsx-runtime.js\");\n/* provided dependency */ var $ = __webpack_require__(/*! jquery */ \"./node_modules/jquery/dist/jquery.js\");\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; return _typeof = \"function\" == typeof Symbol && \"symbol\" == typeof Symbol.iterator ? function (obj) { return typeof obj; } : function (obj) { return obj && \"function\" == typeof Symbol && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }, _typeof(obj); }\n\nfunction _slicedToArray(arr, i) { return _arrayWithHoles(arr) || _iterableToArrayLimit(arr, i) || _unsupportedIterableToArray(arr, i) || _nonIterableRest(); }\n\nfunction _nonIterableRest() { throw new TypeError(\"Invalid attempt to destructure non-iterable instance.\\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method.\"); }\n\nfunction _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === \"string\") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === \"Object\" && o.constructor) n = o.constructor.name; if (n === \"Map\" || n === \"Set\") return Array.from(o); if (n === \"Arguments\" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }\n\nfunction _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }\n\nfunction _iterableToArrayLimit(arr, i) { var _i = arr == null ? null : typeof Symbol !== \"undefined\" && arr[Symbol.iterator] || arr[\"@@iterator\"]; if (_i == null) return; var _arr = []; var _n = true; var _d = false; var _s, _e; try { for (_i = _i.call(arr); !(_n = (_s = _i.next()).done); _n = true) { _arr.push(_s.value); if (i && _arr.length === i) break; } } catch (err) { _d = true; _e = err; } finally { try { if (!_n && _i[\"return\"] != null) _i[\"return\"](); } finally { if (_d) throw _e; } } return _arr; }\n\nfunction _arrayWithHoles(arr) { if (Array.isArray(arr)) return arr; }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, \"prototype\", { writable: false }); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); Object.defineProperty(subClass, \"prototype\", { writable: false }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } else if (call !== void 0) { throw new TypeError(\"Derived constructors may only return object or undefined\"); } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n // Component for the advanced params input field.\n\n\n\nvar Options = /*#__PURE__*/function (_Component) {\n  _inherits(Options, _Component);\n\n  var _super = _createSuper(Options);\n\n  function Options(props) {\n    var _this;\n\n    _classCallCheck(this, Options);\n\n    _this = _super.call(this, props);\n    _this.state = {\n      preOpts: {},\n      value: '',\n      method: ''\n    };\n    _this.updateBox = _this.updateBox.bind(_assertThisInitialized(_this));\n    _this.optionsJSX = _this.optionsJSX.bind(_assertThisInitialized(_this));\n    _this.showAdvancedOptions = _this.showAdvancedOptions.bind(_assertThisInitialized(_this));\n    return _this;\n  }\n\n  _createClass(Options, [{\n    key: \"updateBox\",\n    value: function updateBox(value) {\n      this.setState({\n        value: value\n      });\n    }\n  }, {\n    key: \"optionsJSX\",\n    value: function optionsJSX() {\n      var _this2 = this;\n\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsxs)(\"span\", {\n        className: \"input-group-btn dropdown\",\n        children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"button\", {\n          className: \"btn bnt-sm btn-default dropdown-toggle\",\n          \"data-toggle\": \"dropdown\",\n          children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"i\", {\n            className: \"fa fa-caret-down\"\n          })\n        }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"ul\", {\n          id: \"advanced-params-dropdown\",\n          className: \"dropdown-menu dropdown-menu-right\",\n          children: Object.entries(this.state.preOpts).map(function (_ref, index) {\n            var _ref2 = _slicedToArray(_ref, 2),\n                key = _ref2[0],\n                value = _ref2[1];\n\n            value = value.join(' ');\n            if (value.trim() === _this2.state.value.trim()) var className = 'yellow-background';\n            return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsxs)(\"li\", {\n              className: className,\n              onClick: function onClick() {\n                return _this2.updateBox(value);\n              },\n              children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsxs)(\"strong\", {\n                children: [key, \":\"]\n              }), \"\\xA0\", value]\n            }, index);\n          })\n        })]\n      });\n    }\n  }, {\n    key: \"showAdvancedOptions\",\n    value: function showAdvancedOptions(e) {\n      var ids = ['blastn', 'tblastn', 'blastp', 'blastx', 'tblastx'];\n      var method = this.state.method.toLowerCase(); // hide options for other algorithms and only show for selected algorithm\n\n      for (var _i2 = 0, _ids = ids; _i2 < _ids.length; _i2++) {\n        var id = _ids[_i2];\n        $(\"#\".concat(id))[id === method ? 'show' : 'hide']();\n      }\n    }\n  }, {\n    key: \"render\",\n    value: function render() {\n      var _this3 = this;\n\n      var classNames = 'form-control';\n\n      if (this.state.value.trim()) {\n        classNames += ' yellow-background';\n      }\n\n      return /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"div\", {\n        className: \"col-md-7\",\n        children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"div\", {\n          className: \"form-group\",\n          children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"div\", {\n            className: \"col-md-12\",\n            children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsxs)(\"div\", {\n              className: \"input-group\",\n              children: [/*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsxs)(\"label\", {\n                className: \"control-label\",\n                htmlFor: \"advanced\",\n                children: [\"Advanced parameters:\", this.state.method && /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"sup\", {\n                  style: {\n                    marginLeft: '2px'\n                  },\n                  children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"a\", {\n                    href: \"\",\n                    onClick: this.showAdvancedOptions,\n                    \"data-toggle\": \"modal\",\n                    \"data-target\": \"#help\",\n                    children: /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"i\", {\n                      className: \"fa fa-question-circle\"\n                    })\n                  })\n                })]\n              }), /*#__PURE__*/(0,react_jsx_runtime__WEBPACK_IMPORTED_MODULE_1__.jsx)(\"input\", {\n                type: \"text\",\n                className: classNames,\n                onChange: function onChange(e) {\n                  return _this3.updateBox(e.target.value);\n                },\n                id: \"advanced\",\n                name: \"advanced\",\n                value: this.state.value,\n                placeholder: \"eg: -evalue 1.0e-5 -num_alignments 100\",\n                title: \"View, and enter advanced parameters.\"\n              }), Object.keys(this.state.preOpts).length > 1 && this.optionsJSX()]\n            })\n          })\n        })\n      });\n    }\n  }]);\n\n  return Options;\n}(react__WEBPACK_IMPORTED_MODULE_0__.Component);\n\n//# sourceURL=webpack://SequenceServer/./public/js/options.js?");
 
 /***/ }),
 
diff --git a/views/_options.erb b/views/_options.erb
deleted file mode 100644
index 06357df0c..000000000
--- a/views/_options.erb
+++ /dev/null
@@ -1,156 +0,0 @@
-<%#
-
-  NOTE: The markup below is displayed in a modal window.  Use less than 70
-        characters per line to preserve formatting.
-%>
-
-<h5>General Search Options</h5>
-<ul class="list-unstyled">
-  <li>
-<pre><%= ERB::Util.h %q|-task <String>
-  Task to execute for the selected BLAST algorithm
-  Options for BLASTN:
-    'blastn'       Traditional BLASTN requiring an exact match of 11 (default)
-    'blastn-short' Optimized BLASTN for query sequences shorter than 50 nucleotides.
-    'megablast'    Traditional megablast used to find very similar sequences (e.g., intraspecies or closely related species).
-    'dc-megablast' Discontiguous megablast used to find somewhat distant sequences (e.g., interspecies).
-    'rmblastn'
-  Options for BLASTP:
-    'blastp'       Standard protein-protein comparisons (default)
-    'blastp-fast'  Faster BLASTP searches using longer words for protein seeding
-    'blastp-short' Optimized BLASTP comparisons for query sequences shorter than 30 residues
-  Options for BLASTX:
-    'blastx'       Standard nucleotide-protein comparisons (default)
-    'blastx-fast'  Optimized nucleotide-protein comparisons
-  Options for TBLASTN:
-    'tblastn'      Standard protein-nucleotide comparisons (default)
-    'tblastn-fast' Optimized protein-nucleotide comparisons
-  Not applicable for TBLASTX| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-evalue <Real>
-  Expectation value (E) threshold for saving hits
-  Default = '10'| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
-  Word size for wordfinder algorithm| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-gapopen <Integer>
-  Cost to open a gap| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-gapextend <Integer>
-  Cost to extend a gap| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-matrix <String>
-  Scoring matrix name (normally BLOSUM62)| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-threshold <Real, >=0>
-  Minimum word score such that the word is added to the BLAST lookup
-  table| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-comp_based_stats <String>
-  Use composition-based statistics for blastp / tblastn:
-      D or d: default (equivalent to 2)
-      0 or F or f: no composition-based statistics
-      1: Composition-based statistics as in NAR 29:2994-3005, 2001
-      2 or T or t : Composition-based score adjustment as in
-      Bioinformatics 21:902-911, 2005, conditioned on sequence
-      properties
-      3: Composition-based score adjustment as in Bioinformatics
-      21:902-911, 2005, unconditionally
-  For programs other than tblastn, must either be absent or be D, F
-  or 0
-  Default = `2'| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
-  Number of database sequences to show one-line descriptions for
-  Default = `500'| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
-  Number of database sequences to show alignments for
-  Default = `250'| %></pre>
-  </li>
-</ul>
-
-<br/>
-
-<h5>Query filtering options</h5>
-<ul class="list-unstyled">
-  <li>
-<pre><%= ERB::Util.h %q|-seg <String>
-  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
-  or 'no' to disable)
-  Default = `no'| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-soft_masking <Boolean>
-  Apply filtering locations as soft masks
-  Default = `false'| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-lcase_masking
-  Use lower case filtering in query and subject sequence(s)?| %></pre>
-  </li>
-</ul>
-
-<br/>
-
-<h5>Restrict search or results</h5>
-<ul class="list-unstyled">
-  <li>
-<pre><%= ERB::Util.h %q|-gilist <String>
-  Restrict search of database to list of GI's
-    * Incompatible with:  negative_gilist, seqidlist, remote, subject,
-  subject_loc| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-seqidlist <String>
-  Restrict search of database to list of SeqId's
-    * Incompatible with:  gilist, negative_gilist, remote, subject,
-  subject_loc| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-negative_gilist <String>
-  Restrict search of database to everything except the listed GIs
-    * Incompatible with:  gilist, seqidlist, remote, subject,
-      subject_loc| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-entrez_query <String>
-  Restrict search with the given Entrez query
-    * Requires:  remote| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-db_soft_mask <String>
-  Filtering algorithm ID to apply to the BLAST database as soft masking
-    * Incompatible with:  subject, subject_loc| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
-  If the query range of a hit is enveloped by that of at least this
-  many higher-scoring hits, delete the hit
-    * Incompatible with:  best_hit_overhang, best_hit_score_edge| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
-  Best Hit algorithm overhang value (recommended value: 0.1)
-    * Incompatible with:  culling_limit| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
-  Best Hit algorithm score edge value (recommended value: 0.1)
-    * Incompatible with:  culling_limit| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
-  Maximum number of aligned sequences to keep| %></pre>
-  </li>
-</ul>
diff --git a/views/blastn_options.erb b/views/blastn_options.erb
new file mode 100644
index 000000000..0e4fdd62b
--- /dev/null
+++ b/views/blastn_options.erb
@@ -0,0 +1,291 @@
+<%#
+  BLASTN ALGORITHM ADVANCED PARAMETERS
+  NOTE: The markup below is displayed in a modal window.  Use less than 70
+        characters per line to preserve formatting.
+%>
+
+<h5>General Search Options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast' 'megablast' 'rmblastn'>
+  Task to execute
+  Default = 'megablast'|%></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-evalue <Real>
+  Expectation value (E) threshold for saving hits
+  Default = '10' (1000 for blastn-short)| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
+  Word size for wordfinder algorithm (length of best perfect match)| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapopen <Integer>
+  Cost to open a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapextend <Integer>
+  Cost to extend a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-penalty <Integer, <=0>
+  Penalty for a nucleotide mismatch| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-reward <Integer, >=0>
+  Reward for a nucleotide match| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-use_index <Boolean>
+  Use MegaBLAST database index
+  Default = 'false'| %></pre>
+  </li>
+</ul>
+  <br />
+
+<h5>Formatting Options</h5>
+<ul class="list-unstyled">
+   <li>
+<pre><%= ERB::Util.h %q|-show_gis
+  Show NCBI GIs in deflines?| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
+  Number of database sequences to show one-line descriptions for
+  Not applicable for outfmt > 4
+  Default = '500'
+  * Incompatible with:  max_target_seqs| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
+  Number of database sequences to show alignments for
+  Default = '250'
+  * Incompatible with:  max_target_seqs| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -line_length <Integer, >=1>
+  Line length for formatting alignments
+  Not applicable for outfmt > 4
+  Default = '60'| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Query filtering options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-dust <String>
+  Filter query sequence with DUST (Format: 'yes', 'level window linker', or
+   'no' to disable) 
+  Default = '20 64 1' ('no' for blastn-short)| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-soft_masking <Boolean>
+  Apply filtering locations as soft masks
+  Default = 'true'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-lcase_masking
+  Use lower case filtering in query and subject sequence(s)?| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Restrict search or results</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-gilist <String>
+  Restrict search of database to list of GIs
+  * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-seqidlist <String>
+  Restrict search of database to list of SeqIDs
+  * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_gilist <String>
+  Restrict search of database to everything except the specified GIs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_seqidlist <String>
+  Restrict search of database to everything except the specified SeqIDs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+  <li>
+<pre><%= ERB::Util.h %q|-taxids <String>
+  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
+  * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_taxids <String>
+  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-taxidlist <String>
+  Restrict search of database to include only the specified taxonomy IDs
+  * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_taxidlist <String>
+  Restrict search of database to everything except the specified taxonomy IDs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-entrez_query <String>
+  Restrict search with the given Entrez query
+  * Requires:  remote| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_soft_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as soft masking
+  * Incompatible with:  db_hard_mask, subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_hard_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as hard masking
+  * Incompatible with:  db_soft_mask, subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-perc_identity <Real, 0..100>
+  Percent identity| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
+  Percent query coverage per hsp| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
+  Set maximum number of HSPs per subject sequence to save for each query| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
+  If the query range of a hit is enveloped by that of at least this
+  many higher-scoring hits, delete the hit
+  * Incompatible with:  best_hit_overhang, best_hit_score_edge| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
+  Best Hit algorithm overhang value (recommended value: 0.1)
+  * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
+  Best Hit algorithm score edge value (recommended value: 0.1)
+  * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-subject_besthit
+  Turn on best hit per subject sequence| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
+  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
+  Default = '500'
+  * Incompatible with:  num_descriptions, num_alignments| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Discontiguous MegaBLAST options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-template_type <String, `coding', `coding_and_optimal', `optimal'>
+  Discontiguous MegaBLAST template type
+  * Requires:  template_length| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-template_length <Integer, Permissible values: '16' '18' '21' >
+  Discontiguous MegaBLAST template length
+  * Requires:  template_type| %></pre>
+  </li>
+
+</ul>
+
+<br/>
+
+<h5>Statistical options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-dbsize <Int8>
+  Effective length of the database| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-searchsp <Int8, >=0>
+  Effective length of the search space| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Extension options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_ungap <Real>
+  X-dropoff value (in bits) for ungapped extensions| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_gap <Real>
+  X-dropoff value (in bits) for preliminary gapped extensions| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_gap_final <Real>
+  X-dropoff value (in bits) for final gapped alignment| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-no_greedy
+  Use non-greedy dynamic programming extension| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-min_raw_gapped_score <Integer>
+  Minimum raw gapped score to keep an alignment in the preliminary gapped and
+   traceback stages| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-ungapped
+  Perform ungapped alignment only?| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-window_size <Integer, >=0>
+  Multiple hits window size, use 0 to specify 1-hit algorithm| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-off_diagonal_range <Integer, >=0>
+  Number of off-diagonals to search for the 2nd hit, use 0 to turn off
+  Default = `0'| %></pre>
+  </li>
+ 
+</ul>
+<br/>
+
+<h5>Miscellaneous options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-parse_deflines <Real>
+  Should the query and subject defline(s) be parsed?| %></pre>
+  </li>
+  
+</ul>
diff --git a/views/blastp_options.erb b/views/blastp_options.erb
new file mode 100644
index 000000000..5b629bf11
--- /dev/null
+++ b/views/blastp_options.erb
@@ -0,0 +1,288 @@
+<%#
+  BLASTP ALGORITHM ADVANCED PARAMETERS
+  NOTE: The markup below is displayed in a modal window.  Use less than 70
+        characters per line to preserve formatting.
+%>
+
+<h5>General Search Options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short'>
+  Task to execute
+  Default = 'blastp'|%></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-evalue <Real>
+  Expectation value (E) threshold for saving hits
+  Default = '10'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
+  Word size for wordfinder algorithm| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapopen <Integer>
+  Cost to open a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapextend <Integer>
+  Cost to extend a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-matrix <String>
+  Scoring matrix name (normally BLOSUM62)| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-threshold <Real, >=0>
+  Minimum word score such that the word is added to the BLAST lookup table| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-comp_based_stats <String>
+  Use composition-based statistics:
+      D or d: default (equivalent to 2)
+      0 or F or f: no composition-based statistics
+      1: Composition-based statistics as in NAR 29:2994-3005, 2001
+      2 or T or t : Composition-based score adjustment as in
+      Bioinformatics 21:902-911, 2005, conditioned on sequence
+      properties
+      3: Composition-based score adjustment as in Bioinformatics
+      21:902-911, 2005, unconditionally
+  Default = '2'| %></pre>
+  </li>
+  </ul>
+  <br />
+
+<h5>Formatting Options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
+  Number of database sequences to show one-line descriptions for
+  Not applicable for outfmt > 4
+  Default = '500'
+  * Incompatible with:  max_target_seqs| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
+  Number of database sequences to show alignments for
+  Default = '250'
+  * Incompatible with:  max_target_seqs| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -sorthits <Integer, (>=0 and =<4)>
+  Sorting option for hits:
+   alignment view options:
+     0 = Sort by evalue,
+     1 = Sort by bit score,
+     2 = Sort by total score,
+     3 = Sort by percent identity,
+     4 = Sort by query coverage
+   Not applicable for outfmt > 4| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -sorthsps <Integer, (>=0 and =<4)>
+  Sorting option for hps:
+     0 = Sort by hsp evalue,
+     1 = Sort by hsp score,
+     2 = Sort by hsp query start,
+     3 = Sort by hsp percent identity,
+     4 = Sort by hsp subject start
+   Not applicable for outfmt != 0| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Query filtering options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-seg <String>
+  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
+  or 'no' to disable)
+  Default = 'no'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-soft_masking <Boolean>
+  Apply filtering locations as soft masks
+  Default = 'false'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-lcase_masking
+  Use lower case filtering in query and subject sequence(s)?| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Restrict search or results</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-gilist <String>
+  Restrict search of database to list of GIs
+  * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-seqidlist <String>
+  Restrict search of database to list of SeqIDs
+  * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_gilist <String>
+  Restrict search of database to everything except the specified GIs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_seqidlist <String>
+  Restrict search of database to everything except the specified SeqIDs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+  <li>
+<pre><%= ERB::Util.h %q|-taxids <String>
+  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
+  * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_taxids <String>
+  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-taxidlist <String>
+  Restrict search of database to include only the specified taxonomy IDs
+  * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_taxidlist <String>
+  Restrict search of database to everything except the specified taxonomy IDs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -ipglist <String>
+  Restrict search of database to list of IPGs
+  * Incompatible with:  subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -negative_ipglist <String>
+  Restrict search of database to everything except the specified IPGs
+  * Incompatible with:  subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-entrez_query <String>
+  Restrict search with the given Entrez query
+  * Requires:  remote| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_soft_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as soft masking
+  * Incompatible with:  db_hard_mask, subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_hard_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as hard masking
+  * Incompatible with:  db_soft_mask, subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
+  Percent query coverage per hsp| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
+  Set maximum number of HSPs per subject sequence to save for each query| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
+  If the query range of a hit is enveloped by that of at least this
+  many higher-scoring hits, delete the hit
+  * Incompatible with:  best_hit_overhang, best_hit_score_edge| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
+  Best Hit algorithm overhang value (recommended value: 0.1)
+  * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
+  Best Hit algorithm score edge value (recommended value: 0.1)
+  * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-subject_besthit
+  Turn on best hit per subject sequence| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
+  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
+  Default = '500'
+  * Incompatible with:  num_descriptions, num_alignments| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Statistical options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-dbsize <Int8>
+  Effective length of the database| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-searchsp <Int8, >=0>
+  Effective length of the search space| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Extension options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_ungap <Real>
+  X-dropoff value (in bits) for ungapped extensions| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_gap <Real>
+  X-dropoff value (in bits) for preliminary gapped extensions| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_gap_final <Real>
+  X-dropoff value (in bits) for final gapped alignment| %></pre>
+  </li>
+  <li>
+  <pre><%= ERB::Util.h %q|-window_size <Integer, >=0>
+  Multiple hits window size, use 0 to specify 1-hit algorithm| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-ungapped
+  Perform ungapped alignment only?| %></pre>
+  </li>
+</ul>
+<br/>
+
+<h5>Miscellaneous options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-parse_deflines <Real>
+  Should the query and subject defline(s) be parsed?| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-use_sw_tback <Real>
+  Compute locally optimal Smith-Waterman alignments?| %></pre>
+  </li>
+  
+</ul>
diff --git a/views/blastx_options.erb b/views/blastx_options.erb
new file mode 100644
index 000000000..db34f0bb8
--- /dev/null
+++ b/views/blastx_options.erb
@@ -0,0 +1,318 @@
+<%#
+  BLASTX ALGORITHM ADVANCED PARAMETERS
+  NOTE: The markup below is displayed in a modal window.  Use less than 70
+        characters per line to preserve formatting.
+%>
+
+<h5>Input Query Options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-strand <String, `both', `minus', `plus'>
+  Query strand(s) to search against database/subject
+  Default = 'both'|%></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-query_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
+  Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/
+   taxonomyhome.html/index.cgi?chapter=cgencodes for details)
+  Default = '1'|%></pre>
+  </li>
+</ul>
+<br />
+
+<h5>General Search Options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-task <String, Permissible values: 'blastx' 'blastx-fast'>
+  Task to execute
+  Default = 'blastx'|%></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-evalue <Real>
+  Expectation value (E) threshold for saving hits
+  Default = '10'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
+  Word size for wordfinder algorithm| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapopen <Integer>
+  Cost to open a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapextend <Integer>
+  Cost to extend a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_intron_length <Integer, >=0>
+  Length of the largest intron allowed in a translated nucleotide sequence when 
+   linking multiple distinct alignments 
+  Default = '0'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-matrix <String>
+  Scoring matrix name (normally BLOSUM62)| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-threshold <Real, >=0>
+  Minimum word score such that the word is added to the BLAST lookup table| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-comp_based_stats <String>
+  Use composition-based statistics:
+      D or d: default (equivalent to 2)
+      0 or F or f: no composition-based statistics
+      1: Composition-based statistics as in NAR 29:2994-3005, 2001
+      2 or T or t : Composition-based score adjustment as in
+      Bioinformatics 21:902-911, 2005, conditioned on sequence
+      properties
+      3: Composition-based score adjustment as in Bioinformatics
+      21:902-911, 2005, unconditionally
+  Default = '2'| %></pre>
+  </li>
+  </ul>
+  <br />
+
+<h5>Formatting Options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-show_gis
+  Show NCBI GIs in deflines?| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
+  Number of database sequences to show one-line descriptions for
+  Not applicable for outfmt > 4
+  Default = '500'
+  * Incompatible with:  max_target_seqs| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
+  Number of database sequences to show alignments for
+  Default = '250'
+  * Incompatible with:  max_target_seqs| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -sorthits <Integer, (>=0 and =<4)>
+  Sorting option for hits:
+   alignment view options:
+     0 = Sort by evalue,
+     1 = Sort by bit score,
+     2 = Sort by total score,
+     3 = Sort by percent identity,
+     4 = Sort by query coverage
+   Not applicable for outfmt > 4| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -sorthsps <Integer, (>=0 and =<4)>
+  Sorting option for hps:
+     0 = Sort by hsp evalue,
+     1 = Sort by hsp score,
+     2 = Sort by hsp query start,
+     3 = Sort by hsp percent identity,
+     4 = Sort by hsp subject start
+   Not applicable for outfmt != 0| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Query filtering options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-seg <String>
+  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
+  or 'no' to disable)
+  Default = '12 2.2 2.5'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-soft_masking <Boolean>
+  Apply filtering locations as soft masks
+  Default = 'false'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-lcase_masking
+  Use lower case filtering in query and subject sequence(s)?| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Restrict search or results</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-gilist <String>
+  Restrict search of database to list of GIs
+  * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-seqidlist <String>
+  Restrict search of database to list of SeqIDs
+  * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_gilist <String>
+  Restrict search of database to everything except the specified GIs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_seqidlist <String>
+  Restrict search of database to everything except the specified SeqIDs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+  <li>
+<pre><%= ERB::Util.h %q|-taxids <String>
+  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
+  * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_taxids <String>
+  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-taxidlist <String>
+  Restrict search of database to include only the specified taxonomy IDs
+  * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_taxidlist <String>
+  Restrict search of database to everything except the specified taxonomy IDs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -ipglist <String>
+  Restrict search of database to list of IPGs
+  * Incompatible with:  subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -negative_ipglist <String>
+  Restrict search of database to everything except the specified IPGs
+  * Incompatible with:  subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-entrez_query <String>
+  Restrict search with the given Entrez query
+  * Requires:  remote| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_soft_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as soft masking
+  * Incompatible with:  db_hard_mask, subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_hard_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as hard masking
+  * Incompatible with:  db_soft_mask, subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
+  Percent query coverage per hsp| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
+  Set maximum number of HSPs per subject sequence to save for each query| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
+  If the query range of a hit is enveloped by that of at least this
+  many higher-scoring hits, delete the hit
+  * Incompatible with:  best_hit_overhang, best_hit_score_edge| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
+  Best Hit algorithm overhang value (recommended value: 0.1)
+  * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
+  Best Hit algorithm score edge value (recommended value: 0.1)
+  * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-subject_besthit
+  Turn on best hit per subject sequence| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
+  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
+  Default = '500'
+  * Incompatible with:  num_descriptions, num_alignments| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Statistical options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-dbsize <Int8>
+  Effective length of the database| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-searchsp <Int8, >=0>
+  Effective length of the search space| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-sum_stats <Boolean>
+  Use sum statistics| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Extension options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_ungap <Real>
+  X-dropoff value (in bits) for ungapped extensions| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_gap <Real>
+  X-dropoff value (in bits) for preliminary gapped extensions| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_gap_final <Real>
+  X-dropoff value (in bits) for final gapped alignment| %></pre>
+  </li>
+  <li>
+  <pre><%= ERB::Util.h %q|-window_size <Integer, >=0>
+  Multiple hits window size, use 0 to specify 1-hit algorithm| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-ungapped
+  Perform ungapped alignment only?| %></pre>
+  </li>
+</ul>
+<br/>
+
+<h5>Miscellaneous options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-parse_deflines <Real>
+  Should the query and subject defline(s) be parsed?| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-use_sw_tback <Real>
+  Compute locally optimal Smith-Waterman alignments?| %></pre>
+  </li>
+  
+</ul>
diff --git a/views/layout.erb b/views/layout.erb
index 1d3eb3600..b8eb35530 100644
--- a/views/layout.erb
+++ b/views/layout.erb
@@ -103,34 +103,6 @@
     </div> <!-- /container -->
   </div>
 
-  <div
-    class="modal fade" id="help"
-    tabindex="-1">
-    <div
-      class="modal-dialog modal-lg">
-      <div
-        class="modal-content">
-        <div
-          class="modal-header">
-          <h3>Advanced Options</h3>
-        </div>
-        <div
-          class="modal-body">
-          <%= erb :_options %>
-        </div>
-        <div
-          class="modal-footer">
-          <button
-            type="button"
-            class="btn btn-default btn-primary"
-            data-dismiss="modal">
-            Got it!
-          </button>
-        </div>
-      </div>
-    </div>
-  </div> <!-- advanced options -->
-
   <!-- twitter -->
   <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0];if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src="//platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
 </body>
diff --git a/views/search.erb b/views/search.erb
index 76391b9c5..134aae23c 100644
--- a/views/search.erb
+++ b/views/search.erb
@@ -21,8 +21,23 @@
       </div>
       <div
         class="modal-body">
-        <%= erb :_options %>
+          <div id="tblastn">
+          <%= erb :tblastn_options %>
+          </div>
+          <div id="blastn">
+          <%= erb :blastn_options %>
+          </div>
+          <div id="blastx">
+          <%= erb :blastx_options %>
+          </div>
+          <div id="tblastx">
+          <%= erb :tblastx_options %>
+          </div>
+          <div id="blastp">
+          <%= erb :blastp_options %>
+          </div>
       </div>
+      
       <div
         class="modal-footer">
         <button
diff --git a/views/tblastn_options.erb b/views/tblastn_options.erb
new file mode 100644
index 000000000..2c6e03fc6
--- /dev/null
+++ b/views/tblastn_options.erb
@@ -0,0 +1,266 @@
+<%#
+  TBLASTN ALGORITHM ADVANCED PARAMETERS
+  NOTE: The markup below is displayed in a modal window.  Use less than 70
+        characters per line to preserve formatting.
+%>
+
+<h5>General Search Options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-task <String, Permissible values: 'tblastn' 'tblastn-fast'>
+  Task to execute
+  Default = 'tblastn'|%></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-evalue <Real>
+  Expectation value (E) threshold for saving hits
+  Default = '10'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
+  Word size for wordfinder algorithm| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapopen <Integer>
+  Cost to open a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapextend <Integer>
+  Cost to extend a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
+  Genetic code to use to translate database/subjects (see user manual for details)
+  Default = '1' | %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_intron_length <Integer, >=0>
+  Length of the largest intron allowed in a translated nucleotide sequence when 
+   linking multiple distinct alignments 
+  Default = '0'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-matrix <String>
+  Scoring matrix name (normally BLOSUM62)| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-threshold <Real, >=0>
+  Minimum word score such that the word is added to the BLAST lookup
+  table| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-comp_based_stats <String>
+  Use composition-based statistics for blastp / tblastn:
+      D or d: default (equivalent to 2)
+      0 or F or f: no composition-based statistics
+      1: Composition-based statistics as in NAR 29:2994-3005, 2001
+      2 or T or t : Composition-based score adjustment as in
+      Bioinformatics 21:902-911, 2005, conditioned on sequence
+      properties
+      3: Composition-based score adjustment as in Bioinformatics
+      21:902-911, 2005, unconditionally
+  For programs other than tblastn, must either be absent or be D, F
+  or 0
+  Default = '2'| %></pre>
+  </li>
+  </ul>
+  <br />
+
+<h5>Formatting Options</h5>
+<ul class="list-unstyled">
+   <li>
+<pre><%= ERB::Util.h %q|-show_gis
+  Show NCBI GIs in deflines?| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
+  Number of database sequences to show one-line descriptions for
+  Not applicable for outfmt > 4
+  Default = '500'
+  * Incompatible with:  max_target_seqs| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
+  Number of database sequences to show alignments for
+  Default = '250'
+  * Incompatible with:  max_target_seqs| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Query filtering options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-seg <String>
+  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
+  or 'no' to disable)
+  Default = '12 2.2 2.5'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-soft_masking <Boolean>
+  Apply filtering locations as soft masks
+  Default ='false'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-lcase_masking
+  Use lower case filtering in query and subject sequence(s)?| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Restrict search or results</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-gilist <String>
+  Restrict search of database to list of GIs
+  * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-seqidlist <String>
+  Restrict search of database to list of SeqIDs
+  * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_gilist <String>
+  Restrict search of database to everything except the specified GIs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_seqidlist <String>
+  Restrict search of database to everything except the specified SeqIDs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+  <li>
+<pre><%= ERB::Util.h %q|-taxids <String>
+  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
+  * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_taxids <String>
+  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-taxidlist <String>
+  Restrict search of database to include only the specified taxonomy IDs
+  * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_taxidlist <String>
+  Restrict search of database to everything except the specified taxonomy IDs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-entrez_query <String>
+  Restrict search with the given Entrez query
+  * Requires:  remote| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_soft_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as soft masking
+  * Incompatible with:  db_hard_mask, subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_hard_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as hard masking
+  * Incompatible with:  db_soft_mask, subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
+  Percent query coverage per hsp| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
+  Set maximum number of HSPs per subject sequence to save for each query| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
+  If the query range of a hit is enveloped by that of at least this
+  many higher-scoring hits, delete the hit
+  * Incompatible with:  best_hit_overhang, best_hit_score_edge| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
+  Best Hit algorithm overhang value (recommended value: 0.1)
+  * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
+  Best Hit algorithm score edge value (recommended value: 0.1)
+  * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-subject_besthit
+  Turn on best hit per subject sequence| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
+  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
+  Default = '500'
+  * Incompatible with:  num_descriptions, num_alignments| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Statistical options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-dbsize <Int8>
+  Effective length of the database| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-searchsp <Int8, >=0>
+  Effective length of the search space| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-sum_stats <Boolean>
+  Use sum statistics| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Extension options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_ungap <Real>
+  X-dropoff value (in bits) for ungapped extensions| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_gap <Real>
+  X-dropoff value (in bits) for preliminary gapped extensions| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_gap_final <Real>
+  X-dropoff value (in bits) for final gapped alignment| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-ungapped
+  Perform ungapped alignment only?| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-window_size <Integer, >=0>
+  Multiple hits window size, use 0 to specify 1-hit algorithm| %></pre>
+  </li>
+ 
+</ul>
diff --git a/views/tblastx_options.erb b/views/tblastx_options.erb
new file mode 100644
index 000000000..fd9509398
--- /dev/null
+++ b/views/tblastx_options.erb
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+<%#
+  TBLASTX ALGORITHM ADVANCED PARAMETERS
+  NOTE: The markup below is displayed in a modal window.  Use less than 70
+        characters per line to preserve formatting.
+%>
+
+<h5>Input Query Options</h5>
+<ul class="list-unstyled">
+<li>
+<pre><%= ERB::Util.h %q|-strand <String, `both', `minus', `plus'>
+  Query strand(s) to search against database/subject
+  Default = 'both'|%></pre>
+  </li>
+<li>
+<pre><%= ERB::Util.h %q|-query_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
+  Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/
+   taxonomyhome.html/index.cgi?chapter=cgencodes for details)
+  Default = '1'|%></pre>
+  </li>
+</ul>
+
+<br />
+
+<h5>General Search Options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-evalue <Real>
+  Expectation value (E) threshold for saving hits
+  Default = '10'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
+  Word size for wordfinder algorithm| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_intron_length <Integer, >=0>
+  Length of the largest intron allowed in a translated nucleotide sequence when 
+   linking multiple distinct alignments 
+  Default = '0'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-matrix <String>
+  Scoring matrix name (normally BLOSUM62)| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-threshold <Real, >=0>
+  Minimum word score such that the word is added to the BLAST lookup table| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
+  Genetic code to use to translate database/subjects (see user manual for details)
+  Default = '1' | %></pre>
+  </li>
+</ul>
+  <br />
+
+<h5>Formatting Options</h5>
+<ul class="list-unstyled">
+   <li>
+<pre><%= ERB::Util.h %q|-show_gis
+  Show NCBI GIs in deflines?| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
+  Number of database sequences to show one-line descriptions for
+  Not applicable for outfmt > 4
+  Default = '500'
+  * Incompatible with:  max_target_seqs| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
+  Number of database sequences to show alignments for
+  Default = '250'
+  * Incompatible with:  max_target_seqs| %></pre>
+  </li>
+    <li>
+<pre><%= ERB::Util.h %q| -sorthits <Integer, (>=0 and =<4)>
+  Sorting option for hits:
+   alignment view options:
+     0 = Sort by evalue,
+     1 = Sort by bit score,
+     2 = Sort by total score,
+     3 = Sort by percent identity,
+     4 = Sort by query coverage
+   Not applicable for outfmt > 4| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -sorthsps <Integer, (>=0 and =<4)>
+  Sorting option for hps:
+     0 = Sort by hsp evalue,
+     1 = Sort by hsp score,
+     2 = Sort by hsp query start,
+     3 = Sort by hsp percent identity,
+     4 = Sort by hsp subject start
+   Not applicable for outfmt != 0| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Query filtering options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-seg <String>
+  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
+  or 'no' to disable)
+  Default = '12 2.2 2.5'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-soft_masking <Boolean>
+  Apply filtering locations as soft masks
+  Default ='false'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-lcase_masking
+  Use lower case filtering in query and subject sequence(s)?| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Restrict search or results</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-gilist <String>
+  Restrict search of database to list of GIs
+  * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-seqidlist <String>
+  Restrict search of database to list of SeqIDs
+  * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_gilist <String>
+  Restrict search of database to everything except the specified GIs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_seqidlist <String>
+  Restrict search of database to everything except the specified SeqIDs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+  <li>
+<pre><%= ERB::Util.h %q|-taxids <String>
+  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
+  * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_taxids <String>
+  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-taxidlist <String>
+  Restrict search of database to include only the specified taxonomy IDs
+  * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
+   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_taxidlist <String>
+  Restrict search of database to everything except the specified taxonomy IDs
+  * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
+   negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
+   subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-entrez_query <String>
+  Restrict search with the given Entrez query
+  * Requires:  remote| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_soft_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as soft masking
+  * Incompatible with:  db_hard_mask, subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_hard_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as hard masking
+  * Incompatible with:  db_soft_mask, subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
+  Percent query coverage per hsp| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
+  Set maximum number of HSPs per subject sequence to save for each query| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
+  If the query range of a hit is enveloped by that of at least this
+  many higher-scoring hits, delete the hit
+  * Incompatible with:  best_hit_overhang, best_hit_score_edge| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
+  Best Hit algorithm overhang value (recommended value: 0.1)
+  * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
+  Best Hit algorithm score edge value (recommended value: 0.1)
+  * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-subject_besthit
+  Turn on best hit per subject sequence| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
+  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
+  Default = '500'
+  * Incompatible with:  num_descriptions, num_alignments| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Statistical options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-dbsize <Int8>
+  Effective length of the database| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-searchsp <Int8, >=0>
+  Effective length of the search space| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-sum_stats <Boolean>
+  Use sum statistics| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Search Strategy options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-import_search_strategy <File_In>
+  Search strategy to use
+  * Incompatible with:  export_search_strategy| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-export_search_strategy <File_Out>
+  File name to record the search strategy used
+  * Incompatible with:  import_search_strategy| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-sum_stats <Boolean>
+  Use sum statistics| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h5>Extension options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-xdrop_ungap <Real>
+  X-dropoff value (in bits) for ungapped extensions| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-window_size <Integer, >=0>
+  Multiple hits window size, use 0 to specify 1-hit algorithm| %></pre>
+  </li>
+ 
+</ul>
+<br />
+<h5>Miscellaneous options</h5>
+<ul class="list-unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-parse_deflines <Real>
+  Should the query and subject defline(s) be parsed?| %></pre>
+  </li>
+</ul>