diff --git a/.gitignore b/.gitignore
index ab3512e..104b5e3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,4 +26,7 @@ api/data/
 
 # Test files
 tests/.env
-.pytest_cache
\ No newline at end of file
+.pytest_cache
+
+# Temp
+temp/
\ No newline at end of file
diff --git a/api/draw_utils.py b/api/draw_utils.py
index cf14e78..9410efd 100644
--- a/api/draw_utils.py
+++ b/api/draw_utils.py
@@ -252,7 +252,7 @@ def mol_to_image(
         [a.SetAtomMapNum(0) for a in mol.GetAtoms()]
     if show_atom_indices:
         mol.UpdatePropertyCache(False)
-    if abbreviate and not highlight_atoms and not highlight_bonds and clear_map:
+    if abbreviate and not highlight_atoms and not highlight_bonds and clear_map and not show_atom_indices:
         mol.UpdatePropertyCache(False)
         mol = rdAbbreviations.CondenseMolAbbreviations(mol, ABBREVIATIONS)
     if update:
@@ -494,7 +494,7 @@ def molecule_smiles_to_image(
     """
     if not highlight and split:
         mols = [Chem.MolFromSmarts(smi) if show_atom_indices else Chem.MolFromSmiles(smi) for smi in smiles.split(".")]
-        images = [mol_to_image(mol, svg=svg, transparent=transparent, abbreviate=abbreviate, reference=reference, **kwargs) for mol in mols]
+        images = [mol_to_image(mol, svg=svg, transparent=transparent, abbreviate=abbreviate, reference=reference, show_atom_indices=show_atom_indices, **kwargs) for mol in mols]
         return combine_images_horizontally(images, transparent=transparent, return_png=return_png)
 
     mol = Chem.MolFromSmarts(smiles) if show_atom_indices else Chem.MolFromSmiles(smiles)
@@ -539,51 +539,63 @@ def molecule_smiles_to_image(
             print("Unable to determine atom highlights using specified reacting atoms. Drawing without highlights.")
             tb.print_exc()
 
-    return mol_to_image(mol, svg=svg, transparent=transparent, return_png=return_png, abbreviate=abbreviate, reference=reference, **kwargs)
+    return mol_to_image(mol, svg=svg, transparent=transparent, return_png=return_png, abbreviate=abbreviate, reference=reference, show_atom_indices=show_atom_indices, **kwargs)
 
 
 def determine_highlight_colors(mol, frag_map, frag_idx=None):
     """
     Determine highlight colors for reactants and products based on atom map.
 
-    Adapted from RDKit MolDraw2D.DrawReaction
-    https://github.com/rdkit/rdkit/blob/Release_2020_09_5/Code/GraphMol/MolDraw2D/MolDraw2D.cpp#L547
-
-    If ``frag_idx`` is specified:
-        * The molecule is considered a reactant fragment
-        * All atoms in the molecule will be highlighted using the same color
-        * ``frag_map`` will be updated in place
-
-    Otherwise:
-        * The molecule is considered a product fragment
-        * Atoms will be colored based the contents of ``frag_map``
-        * ``frag_map`` will not be altered
+    More robust behavior:
+      - When frag_idx is provided (building phase): assign every mapped atom's mapno
+        to frag_idx in frag_map (overwriting if already present).
+      - When frag_idx is None (drawing phase): only highlight atoms whose mapno exists
+        in frag_map (skip unknown map numbers instead of raising KeyError).
 
     Args:
         mol (Chem.Mol): molecule object to analyze
-        frag_map (dict): mapping from atom map number to fragment index
-        frag_idx (int, optional): current fragment index
+        frag_map (dict[int, int]): mapping from atom map number -> fragment index
+        frag_idx (int, optional): current fragment index when building frag_map
 
     Returns:
-        dict: containing highlight kwargs for ``mol_to_image``
+        dict: highlight kwargs for mol_to_image
     """
     highlight_atoms = []
     highlight_bonds = []
     highlight_atom_colors = {}
     highlight_bond_colors = {}
+
     for atom in mol.GetAtoms():
         mapno = atom.GetAtomMapNum()
-        if mapno:
-            idx = atom.GetIdx()
-            if frag_idx is not None:
-                frag_map[mapno] = frag_idx
-            highlight_atoms.append(idx)
-            highlight_atom_colors[idx] = HIGHLIGHT_COLORS[frag_map[mapno] % len(HIGHLIGHT_COLORS)]
-            for atom2 in atom.GetNeighbors():
-                if atom2.GetIdx() < idx and highlight_atom_colors.get(atom2.GetIdx()) == highlight_atom_colors[idx]:
-                    bond_idx = mol.GetBondBetweenAtoms(idx, atom2.GetIdx()).GetIdx()
-                    highlight_bonds.append(bond_idx)
-                    highlight_bond_colors[bond_idx] = highlight_atom_colors[idx]
+        if not mapno:
+            continue  # RDKit uses 0 for "no mapping"
+
+        # Build-phase: record map number -> fragment index
+        if frag_idx is not None:
+            frag_map[mapno] = frag_idx
+
+        # Draw-phase: if we don't know this map number, skip it (don't crash)
+        frag = frag_map.get(mapno)
+        if frag is None:
+            continue
+
+        idx = atom.GetIdx()
+        color = HIGHLIGHT_COLORS[frag % len(HIGHLIGHT_COLORS)]
+
+        highlight_atoms.append(idx)
+        highlight_atom_colors[idx] = color
+
+        # Highlight bonds between same-colored neighboring atoms
+        for atom2 in atom.GetNeighbors():
+            j = atom2.GetIdx()
+            if j < idx and highlight_atom_colors.get(j) == color:
+                bond = mol.GetBondBetweenAtoms(idx, j)
+                if bond is None:
+                    continue
+                bond_idx = bond.GetIdx()
+                highlight_bonds.append(bond_idx)
+                highlight_bond_colors[bond_idx] = color
+
     return {
         "highlight_atoms": highlight_atoms,
         "highlight_bonds": highlight_bonds,
@@ -591,8 +603,7 @@ def determine_highlight_colors(mol, frag_map, frag_idx=None):
         "highlight_bond_colors": highlight_bond_colors,
     }
 
-
-
+    
 def reaction_smiles_to_image(smiles, svg=True, transparent=True, return_png=True, retro=False, highlight=False, align=False, plus=True, update=True, show_atom_indices=False,**kwargs):
     """
     Create image of the provided reaction SMILES string. Omits agents.
@@ -637,10 +648,12 @@ def reaction_smiles_to_image(smiles, svg=True, transparent=True, return_png=True
         if plus and i > 0:
             images.append(draw_plus(svg=svg, transparent=transparent))
         smiles = Chem.MolToSmarts(mol) if show_atom_indices else Chem.MolToSmiles(mol)
-        if smiles.count(".") > 1:
+        # Only split when NOT highlighting; splitting breaks highlight atom indices
+        if (not highlight) and smiles.count(".") > 1:
             images.append(molecule_smiles_to_image(smiles, svg=svg, transparent=transparent, **kwargs))
         else:
-            images.append(mol_to_image(mol, svg=svg, transparent=transparent, update=update, show_atom_indices=show_atom_indices, **kwargs))
+            images.append(mol_to_image(mol, svg=svg, transparent=transparent, update=update,
+                                    show_atom_indices=show_atom_indices, **kwargs))
 
     images.append(draw_arrow(retro=retro, svg=svg, transparent=transparent))
 
diff --git a/api/environment.yml b/api/environment.yml
index f8dcbf7..54cde61 100644
--- a/api/environment.yml
+++ b/api/environment.yml
@@ -5,7 +5,7 @@ channels:
 dependencies:
   - svgutils
   - python=3.12
-  - rdkit=2024.3.5
+  - rdkit=2025.03.2
   - networkx
   - pip
   - pip:
diff --git a/api/server.py b/api/server.py
index 2f94b74..957319b 100644
--- a/api/server.py
+++ b/api/server.py
@@ -268,7 +268,8 @@ class Availability(BaseModel):
 class InputFile(BaseModel):
     synth_graph: Optional[SynthGraph] = None
     evidence_synth_graph: Optional[SynthGraph] = None
-    predictive_synth_graph: Optional[SynthGraph] = None
+    predicted_synth_graph: Optional[SynthGraph] = None
+    predictive_synth_graph: Optional[SynthGraph] = None  # Deprecated: Use predicted_synth_graph
     routes: Optional[List[Route]] = None
     availability: Optional[list[Availability]] = None
 
@@ -521,6 +522,7 @@ async def rxsmiles_to_svg_endpoint(rxsmiles: str = 'CCO.CC(=O)O>>CC(=O)OCC.O', h
           <text x="10" y="50" font-size="32" fill="black">Unable to generate reaction SVG</text>
         </svg>
         """.strip()
+        logger.error(f"Error generating SVG for rxsmiles {rxsmiles}: {e}")
 
     if base64_encode:
         svg = base64.b64encode(svg.encode('utf-8')).decode('utf-8')
@@ -669,7 +671,7 @@ def flatten_dict(d, parent_key='', sep='_'):
     return dict(items)
 
 
-def convert_to_cytoscape_json(aicp_graph, synth_graph_key="synth_graph", convert_route=False, predicted_route=False, route_index=0):
+def convert_to_cytoscape_json(aicp_graph, synth_graph_key="synth_graph", convert_route=False, is_predicted=False, route_index=0):
     # Try to get the specified graph, with fallback logic similar to frontend
     synth_graph = None
     
@@ -679,10 +681,12 @@ def convert_to_cytoscape_json(aicp_graph, synth_graph_key="synth_graph", convert
         synth_graph = aicp_graph["synth_graph"]
     elif "evidence_synth_graph" in aicp_graph and aicp_graph["evidence_synth_graph"] is not None:
         synth_graph = aicp_graph["evidence_synth_graph"]
+    elif "predicted_synth_graph" in aicp_graph and aicp_graph["predicted_synth_graph"] is not None:
+        synth_graph = aicp_graph["predicted_synth_graph"]
     elif "predictive_synth_graph" in aicp_graph and aicp_graph["predictive_synth_graph"] is not None:
-        synth_graph = aicp_graph["predictive_synth_graph"]
+        synth_graph = aicp_graph["predictive_synth_graph"]  # Backward compatibility
     else:
-        raise ValueError(f"No synthesis graph found. Looked for: {synth_graph_key}, synth_graph, evidence_synth_graph, predictive_synth_graph")
+        raise ValueError(f"No synthesis graph found. Looked for: {synth_graph_key}, synth_graph, evidence_synth_graph, predicted_synth_graph, predictive_synth_graph")
 
     if convert_route:
         routes = aicp_graph.get("routes", [])
@@ -724,7 +728,7 @@ def convert_to_cytoscape_json(aicp_graph, synth_graph_key="synth_graph", convert
         ]
         aggregated_yield = "N/A"
 
-    if predicted_route:
+    if is_predicted:
         for node in filtered_nodes:
             node_type = node["data"].get("node_type", "")
             if isinstance(node_type, str) and node_type.lower() == "substance":
@@ -758,11 +762,11 @@ def convert_to_cytoscape_json(aicp_graph, synth_graph_key="synth_graph", convert
     # Generate name based on whether this is a route or full graph
     if convert_route:
         # Route name: Include reaction steps, index, and type
-        route_type = "Predicted" if predicted_route else "Evidence"
+        route_type = "Predicted" if is_predicted else "Evidence"
         cytoscape_name = f"{target_inchikey}_SD_{reaction_steps} - Route {route_index} - {route_type}"
     else:
         # Full graph name: Simple format
-        graph_type = "Predicted Graph" if predicted_route else "Evidence Graph"
+        graph_type = "Predicted Graph" if is_predicted else "Evidence Graph"
         cytoscape_name = f"{target_inchikey} - {graph_type}"
 
     return {
@@ -820,7 +824,7 @@ def send_to_cytoscape(
     layout_type: str = "hierarchical",
     send_all_routes: bool = True,
     synth_graph_key: str = "synth_graph",
-    predicted_route: bool = False,
+    is_predicted: bool = False,
     convert_route: bool = False,
     route_index: int = 0,
 ):   
@@ -834,7 +838,7 @@ def send_to_cytoscape(
     - layout_type (str, optional): Layout algorithm name (e.g., "hierarchical"). Defaults to "hierarchical".
     - send_all_routes (bool, optional): If True, sends all routes as separate networks. If False, uses single route/graph mode. Defaults to True.
     - synth_graph_key (str, optional): Key in the input JSON containing the synthesis graph. Defaults to "synth_graph". Auto-detects if not present.
-    - predicted_route (bool, optional): If True, relabels substance nodes (e.g., by InChIKey) and marks network as predicted. Only used when send_all_routes=False.
+    - is_predicted (bool, optional): If True, relabels substance nodes (e.g., by InChIKey) and marks network as predicted. Only used when send_all_routes=False.
     - convert_route (bool, optional): If True, filters the graph to a single route. Only used when send_all_routes=False. Defaults to False.
     - route_index (int, optional): Index into the 'routes' array to select a route. Only used when send_all_routes=False and convert_route=True. Defaults to 0.
 
@@ -863,7 +867,7 @@ def send_to_cytoscape(
                 network_json,
                 synth_graph_key,
                 convert_route,
-                predicted_route,
+                is_predicted,
                 route_index
             )
             return _send_single_network_to_cytoscape(converted_json, layout_type)
@@ -876,14 +880,16 @@ def send_to_cytoscape(
         routes = network_json.get("routes", [])
         results = []
         
-        # First, send all available full graphs (synth_graph, evidence_synth_graph, predictive_synth_graph)
+        # First, send all available full graphs (synth_graph, evidence_synth_graph, predicted_synth_graph)
         graph_types = []
         if "synth_graph" in network_json and network_json["synth_graph"] is not None:
             graph_types.append(("synth_graph", False, "Evidence Synthesis Graph"))
         if "evidence_synth_graph" in network_json and network_json["evidence_synth_graph"] is not None:
             graph_types.append(("evidence_synth_graph", False, "Evidence Synthesis Graph"))
-        if "predictive_synth_graph" in network_json and network_json["predictive_synth_graph"] is not None:
-            graph_types.append(("predictive_synth_graph", True, "Predictive Synthesis Graph"))
+        if "predicted_synth_graph" in network_json and network_json["predicted_synth_graph"] is not None:
+            graph_types.append(("predicted_synth_graph", True, "Predicted Synthesis Graph"))
+        elif "predictive_synth_graph" in network_json and network_json["predictive_synth_graph"] is not None:
+            graph_types.append(("predictive_synth_graph", True, "Predicted Synthesis Graph"))  # Backward compatibility
         
         # Send each full graph
         for graph_key, is_predicted, graph_name in graph_types:
@@ -894,7 +900,7 @@ def send_to_cytoscape(
                     network_json,
                     graph_key,
                     convert_route=False,
-                    predicted_route=is_predicted,
+                    is_predicted=is_predicted,
                     route_index=0
                 )
                 
@@ -940,13 +946,20 @@ def send_to_cytoscape(
                 logger.info(f"Processing route {idx}: {route_name}")
                 
                 # Use the correct graph key based on route type
-                route_graph_key = "predictive_synth_graph" if is_predicted else synth_graph_key
+                # Check predicted_synth_graph first, fallback to predictive_synth_graph for backward compatibility
+                if is_predicted:
+                    if "predicted_synth_graph" in network_json and network_json["predicted_synth_graph"] is not None:
+                        route_graph_key = "predicted_synth_graph"
+                    else:
+                        route_graph_key = "predictive_synth_graph"  # Backward compatibility
+                else:
+                    route_graph_key = synth_graph_key
                 
                 converted_json = convert_to_cytoscape_json(
                     network_json,
                     route_graph_key,
                     convert_route=True,
-                    predicted_route=is_predicted,
+                    is_predicted=is_predicted,
                     route_index=idx
                 )
                 
@@ -1168,7 +1181,7 @@ async def _convert_to_aicp(request: ConvertToAicpRequest) -> dict:
 
         # Return converted graph
         return {
-            "predictive_synth_graph": {
+            "predicted_synth_graph": {
                 "nodes": nodes,
                 "edges": edges
             },
diff --git a/data/hybrid_routes_example.json b/data/hybrid_routes_example.json
index 22ef22f..1d4f6af 100644
--- a/data/hybrid_routes_example.json
+++ b/data/hybrid_routes_example.json
@@ -2707,7 +2707,7 @@
       }
     ]
   },
-  "predictive_synth_graph": {
+  "predicted_synth_graph": {
     "nodes": [
       {
         "node_label": "45427382-fde3-4163-8315-468e47f1ebab",
diff --git a/data/merged_example.json b/data/merged_example.json
new file mode 100644
index 0000000..63414c7
--- /dev/null
+++ b/data/merged_example.json
@@ -0,0 +1,6605 @@
+{
+  "target_molecule_inchikey": "BACODVKOMBXPLL-UHFFFAOYSA-N",
+  "target_molecule_smiles": "O=C(O)c1cc(-c2ccccc2)cc2cc[nH]c12",
+  "reaction_steps": 2,
+  "evidence_routes_success": true,
+  "predicted_routes_success": true,
+  "routes": [
+    {
+      "aggregated_yield": 58.84784878828043,
+      "predicted": false,
+      "route_index": 1,
+      "route_status": "Viable Synthesis Route",
+      "method": "AICP",
+      "route_node_labels": [
+        "RYHBNJHYFVUHQT-UHFFFAOYSA-N",
+        "YSFZPMNRVJTVIV-UHFFFAOYSA-N",
+        "FJDQFPXHSGXQBY-UHFFFAOYSA-L",
+        "HXITXNWTGFUOAU-UHFFFAOYSA-N",
+        "ASPIRE-6958145032533313838",
+        "YJVFFLUZDVXJQI-UHFFFAOYSA-L",
+        "LFQSCWFLJHTTHZ-UHFFFAOYSA-N",
+        "ASPIRE-2097084335487425141",
+        "OKKJLVBELUTLKV-UHFFFAOYSA-N",
+        "BACODVKOMBXPLL-UHFFFAOYSA-N",
+        "XLYOFNOQVPJJNP-UHFFFAOYSA-N",
+        "VZYDZTIPNOBVNC-UHFFFAOYSA-N",
+        "WMFOQBRAJBCJND-UHFFFAOYSA-M",
+        "OTOSIXGMLYKKOW-UHFFFAOYSA-M",
+        "PCHJSUWPFVWCPO-UHFFFAOYSA-N",
+        "AUVSUPMVIZXUOG-UHFFFAOYSA-N",
+        "ASPIRE-4105087716800423292"
+      ]
+    },
+    {
+      "aggregated_yield": 57.61799729751479,
+      "predicted": false,
+      "route_index": 2,
+      "route_status": "Viable Synthesis Route",
+      "method": "AICP",
+      "route_node_labels": [
+        "RYHBNJHYFVUHQT-UHFFFAOYSA-N",
+        "YSFZPMNRVJTVIV-UHFFFAOYSA-N",
+        "NHDIQVFFNDKAQU-UHFFFAOYSA-N",
+        "FJDQFPXHSGXQBY-UHFFFAOYSA-L",
+        "HXITXNWTGFUOAU-UHFFFAOYSA-N",
+        "ASPIRE-6958145032533313838",
+        "YJVFFLUZDVXJQI-UHFFFAOYSA-L",
+        "MZRVEZGGRBJDDB-UHFFFAOYSA-N",
+        "ASPIRE-2672521253083458424",
+        "BACODVKOMBXPLL-UHFFFAOYSA-N",
+        "OKKJLVBELUTLKV-UHFFFAOYSA-N",
+        "XLYOFNOQVPJJNP-UHFFFAOYSA-N",
+        "VZYDZTIPNOBVNC-UHFFFAOYSA-N",
+        "OTOSIXGMLYKKOW-UHFFFAOYSA-M",
+        "VLKZOEOYAKHREP-UHFFFAOYSA-N",
+        "WMFOQBRAJBCJND-UHFFFAOYSA-M",
+        "ASPIRE-4105087716800423292"
+      ]
+    },
+    {
+      "aggregated_yield": 57.61799729751479,
+      "predicted": false,
+      "route_index": 3,
+      "route_status": "Viable Synthesis Route",
+      "method": "AICP",
+      "route_node_labels": [
+        "RYHBNJHYFVUHQT-UHFFFAOYSA-N",
+        "YSFZPMNRVJTVIV-UHFFFAOYSA-N",
+        "NHDIQVFFNDKAQU-UHFFFAOYSA-N",
+        "FJDQFPXHSGXQBY-UHFFFAOYSA-L",
+        "ANUZKYYBDVLEEI-UHFFFAOYSA-N",
+        "HXITXNWTGFUOAU-UHFFFAOYSA-N",
+        "ASPIRE-6958145032533313838",
+        "YJVFFLUZDVXJQI-UHFFFAOYSA-L",
+        "BACODVKOMBXPLL-UHFFFAOYSA-N",
+        "OKKJLVBELUTLKV-UHFFFAOYSA-N",
+        "XLYOFNOQVPJJNP-UHFFFAOYSA-N",
+        "VZYDZTIPNOBVNC-UHFFFAOYSA-N",
+        "OTOSIXGMLYKKOW-UHFFFAOYSA-M",
+        "WMFOQBRAJBCJND-UHFFFAOYSA-M",
+        "ASPIRE-4105087716800423292",
+        "ASPIRE-8090828743022637323"
+      ]
+    },
+    {
+      "predicted": true,
+      "source": "ASKCOS v2",
+      "route_index": 4,
+      "route_node_labels": [
+        "NJSFLYKFAHEEET-UHFFFAOYSA-N",
+        "287c4669-a6a7-42b4-9cd8-403259dc7e36",
+        "BACODVKOMBXPLL-UHFFFAOYSA-N"
+      ]
+    },
+    {
+      "predicted": true,
+      "source": "ASKCOS v2",
+      "route_index": 5,
+      "route_node_labels": [
+        "YVPFHVKOHMYAHB-UHFFFAOYSA-N",
+        "NTIQTKXSDRUAOC-UHFFFAOYSA-M",
+        "659dbbdc-9182-49f0-b217-5978e482cd70",
+        "AAJMEFMGYGSJPA-UHFFFAOYSA-N",
+        "e2b32b2f-925c-44e6-bd73-4a305d8b0b75",
+        "BACODVKOMBXPLL-UHFFFAOYSA-N"
+      ]
+    },
+    {
+      "predicted": true,
+      "source": "ASKCOS v2",
+      "route_index": 6,
+      "route_node_labels": [
+        "SDMOTXWDDFBAMM-UHFFFAOYSA-N",
+        "HXITXNWTGFUOAU-UHFFFAOYSA-N",
+        "3d609715-c3d8-4ad1-a5b0-00f49bd8544b",
+        "VMTPCPGYOUPMEU-UHFFFAOYSA-N",
+        "a71404ab-ef31-4341-b11a-c1f0338c0666",
+        "BACODVKOMBXPLL-UHFFFAOYSA-N"
+      ]
+    }
+  ],
+  "synth_graph": {
+    "nodes": [
+      {
+        "node_label": "BACODVKOMBXPLL-UHFFFAOYSA-N",
+        "node_type": "substance",
+        "uuid": "substance_da2a646a25fc5aa2427dd50c68cc4b86da7fafdd2c912d65e67d2a4db9892a65",
+        "inchikey": "BACODVKOMBXPLL-UHFFFAOYSA-N",
+        "canonical_smiles": "O=C(O)c1cc(-c2ccccc2)cc2cc[nH]c12",
+        "srole": "tm",
+        "route_assembly_type": {
+          "is_predicted": false,
+          "is_evidence": true
+        },
+        "provenance": {
+          "is_in_aicp": false,
+          "is_in_uspto_full": true,
+          "is_in_savi_130k": false,
+          "is_from_askcos": false,
+          "patents": [],
+          "patent_paragraph_nums": []
+        }
+      },
+      {
+        "node_label": "ASPIRE-4105087716800423292",
+        "node_type": "reaction",
+        "uuid": "reaction_96af5b2032390055fe1fb409e44e6201c0bea544e20f29a1f287fb95b52cfe18",
+        "rxid": "ASPIRE-4105087716800423292",
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+          "is_in_savi_130k": null,
+          "is_from_askcos": true,
+          "patents": null,
+          "patent_paragraph_nums": null
+        },
+        "uuid": "REACTANT_OF_19dd9116b04740998b6d1c901415434d",
+        "inchikey": "",
+        "rxid": "",
+        "route_assembly_type": {
+          "is_predicted": true,
+          "is_evidence": false
+        }
+      },
+      {
+        "start_node": "e2b32b2f-925c-44e6-bd73-4a305d8b0b75",
+        "end_node": "BACODVKOMBXPLL-UHFFFAOYSA-N",
+        "edge_label": "e2b32b2f-925c-44e6-bd73-4a305d8b0b75|BACODVKOMBXPLL-UHFFFAOYSA-N",
+        "edge_type": "PRODUCT_OF",
+        "provenance": {
+          "is_in_aicp": null,
+          "is_in_uspto_full": null,
+          "is_in_savi_130k": null,
+          "is_from_askcos": true,
+          "patents": null,
+          "patent_paragraph_nums": null
+        },
+        "uuid": "PRODUCT_OF_d0902c37e022488cad56756b02b9c520",
+        "inchikey": "",
+        "rxid": "",
+        "route_assembly_type": {
+          "is_predicted": true,
+          "is_evidence": false
+        }
+      },
+      {
+        "start_node": "SDMOTXWDDFBAMM-UHFFFAOYSA-N",
+        "end_node": "3d609715-c3d8-4ad1-a5b0-00f49bd8544b",
+        "edge_label": "SDMOTXWDDFBAMM-UHFFFAOYSA-N|3d609715-c3d8-4ad1-a5b0-00f49bd8544b",
+        "edge_type": "REACTANT_OF",
+        "provenance": {
+          "is_in_aicp": null,
+          "is_in_uspto_full": null,
+          "is_in_savi_130k": null,
+          "is_from_askcos": true,
+          "patents": null,
+          "patent_paragraph_nums": null
+        },
+        "uuid": "REACTANT_OF_717451036d7b4363bcaba7ee758c9710",
+        "inchikey": "",
+        "rxid": "",
+        "route_assembly_type": {
+          "is_predicted": true,
+          "is_evidence": false
+        }
+      },
+      {
+        "start_node": "HXITXNWTGFUOAU-UHFFFAOYSA-N",
+        "end_node": "3d609715-c3d8-4ad1-a5b0-00f49bd8544b",
+        "edge_label": "HXITXNWTGFUOAU-UHFFFAOYSA-N|3d609715-c3d8-4ad1-a5b0-00f49bd8544b",
+        "edge_type": "REACTANT_OF",
+        "provenance": {
+          "is_in_aicp": null,
+          "is_in_uspto_full": null,
+          "is_in_savi_130k": null,
+          "is_from_askcos": true,
+          "patents": null,
+          "patent_paragraph_nums": null
+        },
+        "uuid": "REACTANT_OF_b60172d94f0749c8abcb77fc77ed95bc",
+        "inchikey": "",
+        "rxid": "",
+        "route_assembly_type": {
+          "is_predicted": true,
+          "is_evidence": false
+        }
+      },
+      {
+        "start_node": "3d609715-c3d8-4ad1-a5b0-00f49bd8544b",
+        "end_node": "VMTPCPGYOUPMEU-UHFFFAOYSA-N",
+        "edge_label": "3d609715-c3d8-4ad1-a5b0-00f49bd8544b|VMTPCPGYOUPMEU-UHFFFAOYSA-N",
+        "edge_type": "PRODUCT_OF",
+        "provenance": {
+          "is_in_aicp": null,
+          "is_in_uspto_full": null,
+          "is_in_savi_130k": null,
+          "is_from_askcos": true,
+          "patents": null,
+          "patent_paragraph_nums": null
+        },
+        "uuid": "PRODUCT_OF_f397bc579ae942948ceb2baa3955621f",
+        "inchikey": "",
+        "rxid": "",
+        "route_assembly_type": {
+          "is_predicted": true,
+          "is_evidence": false
+        }
+      },
+      {
+        "start_node": "VMTPCPGYOUPMEU-UHFFFAOYSA-N",
+        "end_node": "a71404ab-ef31-4341-b11a-c1f0338c0666",
+        "edge_label": "VMTPCPGYOUPMEU-UHFFFAOYSA-N|a71404ab-ef31-4341-b11a-c1f0338c0666",
+        "edge_type": "REACTANT_OF",
+        "provenance": {
+          "is_in_aicp": null,
+          "is_in_uspto_full": null,
+          "is_in_savi_130k": null,
+          "is_from_askcos": true,
+          "patents": null,
+          "patent_paragraph_nums": null
+        },
+        "uuid": "REACTANT_OF_b0a55ae0acc0498cb418d21ff7dfcf52",
+        "inchikey": "",
+        "rxid": "",
+        "route_assembly_type": {
+          "is_predicted": true,
+          "is_evidence": false
+        }
+      },
+      {
+        "start_node": "a71404ab-ef31-4341-b11a-c1f0338c0666",
+        "end_node": "BACODVKOMBXPLL-UHFFFAOYSA-N",
+        "edge_label": "a71404ab-ef31-4341-b11a-c1f0338c0666|BACODVKOMBXPLL-UHFFFAOYSA-N",
+        "edge_type": "PRODUCT_OF",
+        "provenance": {
+          "is_in_aicp": null,
+          "is_in_uspto_full": null,
+          "is_in_savi_130k": null,
+          "is_from_askcos": true,
+          "patents": null,
+          "patent_paragraph_nums": null
+        },
+        "uuid": "PRODUCT_OF_b3169f31361d4de188b15f519783b7bd",
+        "inchikey": "",
+        "rxid": "",
+        "route_assembly_type": {
+          "is_predicted": true,
+          "is_evidence": false
+        }
+      }
+    ]
+  },
+  "num_routes": 6,
+  "num_evidence_routes": 3,
+  "num_predicted_routes": 3
+}
\ No newline at end of file
diff --git a/ui/src/App.js b/ui/src/App.js
index 3658823..14510b0 100644
--- a/ui/src/App.js
+++ b/ui/src/App.js
@@ -335,7 +335,7 @@ function App() {
       subgraphIndex < aicpGraph.routes.length
     ) {
       let data = aicpGraph;
-      const mappedData = mapGraphDataToCytoscape(data, subgraphIndex);
+      const mappedData = mapGraphDataToCytoscape(data, subgraphIndex, usePredictedGraph);
       updateCytoscapeGraph(mappedData);
       resetReagentOriginalGraph.current = true;
     }
diff --git a/ui/src/components/GraphRetrieval/ExampleGraphs.jsx b/ui/src/components/GraphRetrieval/ExampleGraphs.jsx
index 6f72817..895a715 100644
--- a/ui/src/components/GraphRetrieval/ExampleGraphs.jsx
+++ b/ui/src/components/GraphRetrieval/ExampleGraphs.jsx
@@ -13,6 +13,7 @@ const exampleJsonFiles = [
     askcosRoute: true,
   },
   { name: "Hybrid Routes Example", path: "/data/hybrid_routes_example.json" },
+  { name: "Merged Routes Example", path: "/data/merged_example.json" },
 ];
 
 const ExampleGraphs = () => {
diff --git a/ui/src/components/NetworkSearchMenu.jsx b/ui/src/components/NetworkSearchMenu.jsx
index 763548a..0c9614a 100644
--- a/ui/src/components/NetworkSearchMenu.jsx
+++ b/ui/src/components/NetworkSearchMenu.jsx
@@ -23,6 +23,7 @@ const NetworkSearchMenu = () => {
   const [selectedRetrievalOption, setSelectedRetrievalOption] = useState(
     "json"
   );
+  const [primarySynthGraph, setPrimarySynthGraph] = useState(null);
   const [evidenceSynthGraph, setEvidenceSynthGraph] = useState(null);
   const [predictedSynthGraph, setPredictedSynthGraph] = useState(null);
   const [routeOptions, setRouteOptions] = useState(null);
@@ -42,10 +43,22 @@ const NetworkSearchMenu = () => {
   // When aicpGraph changes, update the synth graph states
   useEffect(() => {
     if (aicpGraph) {
-      setEvidenceSynthGraph(
-        aicpGraph.synth_graph || aicpGraph.evidence_synth_graph || null
-      );
-      setPredictedSynthGraph(aicpGraph.predictive_synth_graph || null);
+      const primary = aicpGraph.synth_graph || null;
+      const evidence = aicpGraph.evidence_synth_graph || null;
+      const predicted = aicpGraph.predicted_synth_graph || aicpGraph.predictive_synth_graph || null;
+      
+      setPrimarySynthGraph(primary);
+      
+      // Only show evidence graph if it exists AND differs from primary synth_graph
+      // (or if primary doesn't exist)
+      const showEvidence = evidence && (!primary || JSON.stringify(evidence) !== JSON.stringify(primary));
+      setEvidenceSynthGraph(showEvidence ? evidence : null);
+      
+      // Only show predicted graph if it exists AND differs from primary synth_graph
+      // (or if primary doesn't exist)
+      const showPredicted = predicted && (!primary || JSON.stringify(predicted) !== JSON.stringify(primary));
+      setPredictedSynthGraph(showPredicted ? predicted : null);
+      
       setRouteOptions(aicpGraph.routes || null);
     }
   }, [aicpGraph]);
@@ -53,6 +66,7 @@ const NetworkSearchMenu = () => {
   // Update dropdownDisabled based on the updated state values
   useEffect(() => {
     const shouldDisable =
+      primarySynthGraph == null &&
       evidenceSynthGraph == null &&
       predictedSynthGraph == null &&
       routeOptions == null;
@@ -66,23 +80,30 @@ const NetworkSearchMenu = () => {
 
       if (routeOptions) {
         onRouteChange("Route 0");
+      } else if (primarySynthGraph) {
+        onRouteChange("PrimarySynthGraph");
       } else if (evidenceSynthGraph) {
         onRouteChange("SynthGraph");
       } else if (predictedSynthGraph) {
-        onRouteChange("PredictiveGraph");
+        onRouteChange("PredictedGraph");
       }
     }
-  }, [evidenceSynthGraph, predictedSynthGraph, routeOptions]);
+  }, [primarySynthGraph, evidenceSynthGraph, predictedSynthGraph, routeOptions]);
 
   // On route change
   const onRouteChange = (value) => {
     setSelectedOption(value);
-    if (value == "SynthGraph") {
+    if (value == "PrimarySynthGraph") {
+      setSubgraphIndex(-3);
+      preserveSubgraphIndexRef.current = true;
+      resetReagentOriginalGraph.current = true;
+      setUsePredictedGraph(false);
+    } else if (value == "SynthGraph") {
       setSubgraphIndex(-1);
       preserveSubgraphIndexRef.current = true;
       resetReagentOriginalGraph.current = true;
       setUsePredictedGraph(false);
-    } else if (value == "PredictiveGraph") {
+    } else if (value == "PredictedGraph") {
       setSubgraphIndex(-2);
       preserveSubgraphIndexRef.current = true;
       resetReagentOriginalGraph.current = true;
@@ -124,13 +145,18 @@ const NetworkSearchMenu = () => {
           onChange={(value) => onRouteChange(value)}
           data-testid="SynthesisRouteDropdown"
         >
+          {aicpGraph && primarySynthGraph && (
+            <Select.Option value="PrimarySynthGraph">
+              Synth Graph
+            </Select.Option>
+          )}
           {aicpGraph && evidenceSynthGraph && (
             <Select.Option value="SynthGraph">
               Evidence Synth Graph
             </Select.Option>
           )}
           {aicpGraph && predictedSynthGraph && (
-            <Select.Option value="PredictiveGraph">
+            <Select.Option value="PredictedGraph">
               Predicted Synth Graph
             </Select.Option>
           )}
diff --git a/ui/src/helpers/commonHelpers.js b/ui/src/helpers/commonHelpers.js
index c1ee7e3..89e0ce2 100644
--- a/ui/src/helpers/commonHelpers.js
+++ b/ui/src/helpers/commonHelpers.js
@@ -75,7 +75,7 @@ export const mapGraphData = (data) => {
   };
 };
 
-export const mapGraphDataToCytoscape = (data, routeIndex = 0) => {
+export const mapGraphDataToCytoscape = (data, routeIndex = 0, usePredictedGraph = false) => {
   const flattenObject = (obj) => {
     return Object.keys(obj).reduce((acc, key) => {
       const value = obj[key];
@@ -89,10 +89,10 @@ export const mapGraphDataToCytoscape = (data, routeIndex = 0) => {
     }, {});
   };
 
-  // Extract evidenceSynthGraph and predictedSynthGraph
-  const evidenceSynthGraph =
-    data.synth_graph || data.evidence_synth_graph || {};
-  const predictedSynthGraph = data.predictive_synth_graph || {};
+  // Extract the different graph types
+  const primarySynthGraph = data.synth_graph || {};
+  const evidenceSynthGraph = data.evidence_synth_graph || {};
+  const predictedSynthGraph = data.predicted_synth_graph || data.predictive_synth_graph || {};
 
   // Extract route_node_labels from the selected subgraph
   const routes = data.routes;
@@ -105,7 +105,20 @@ export const mapGraphDataToCytoscape = (data, routeIndex = 0) => {
     const route = routes[routeIndex];
     const predictedRoute = route["predicted"] || false;
 
-    const graph = predictedRoute ? predictedSynthGraph : evidenceSynthGraph;
+    // Select the appropriate graph:
+    // 1. If predicted route, try predictedSynthGraph first, then fall back to primarySynthGraph
+    // 2. If evidence route, try evidenceSynthGraph first, then fall back to primarySynthGraph
+    let graph;
+    if (predictedRoute) {
+      graph = (predictedSynthGraph.nodes && predictedSynthGraph.nodes.length > 0) 
+        ? predictedSynthGraph 
+        : primarySynthGraph;
+    } else {
+      graph = (evidenceSynthGraph.nodes && evidenceSynthGraph.nodes.length > 0) 
+        ? evidenceSynthGraph 
+        : primarySynthGraph;
+    }
+    
     filteredNodes = graph.nodes || [];
     filteredEdges = graph.edges || [];
 
@@ -123,11 +136,23 @@ export const mapGraphDataToCytoscape = (data, routeIndex = 0) => {
         routeNodeLabels.has(edge.end_node)
     );
   } else if (routeIndex === -1) {
-    filteredNodes = evidenceSynthGraph.nodes;
-    filteredEdges = evidenceSynthGraph.edges;
+    // Evidence synth graph, fall back to primary if needed
+    const graph = (evidenceSynthGraph.nodes && evidenceSynthGraph.nodes.length > 0) 
+      ? evidenceSynthGraph 
+      : primarySynthGraph;
+    filteredNodes = graph.nodes;
+    filteredEdges = graph.edges;
   } else if (routeIndex === -2) {
-    filteredNodes = predictedSynthGraph.nodes;
-    filteredEdges = predictedSynthGraph.edges;
+    // Predicted synth graph, fall back to primary if needed
+    const graph = (predictedSynthGraph.nodes && predictedSynthGraph.nodes.length > 0) 
+      ? predictedSynthGraph 
+      : primarySynthGraph;
+    filteredNodes = graph.nodes;
+    filteredEdges = graph.edges;
+  } else if (routeIndex === -3) {
+    // Use the primary synth_graph
+    filteredNodes = primarySynthGraph.nodes;
+    filteredEdges = primarySynthGraph.edges;
   } else {
     throw new Error("Invalid subgraph index.");
   }
@@ -162,6 +187,8 @@ export const mapGraphDataToCytoscape = (data, routeIndex = 0) => {
         evidence_conditions_info: flatNode.evidence_conditions_info ?? {},
         predicted_conditions_info: flatNode.predicted_conditions_info ?? {},
       },
+      // Add class for predicted target molecules
+      classes: flatNode.srole === "tm" && usePredictedGraph ? "predicted-tm" : "",
     };
   });
 
@@ -473,6 +500,12 @@ export const cyStyles = [
       "border-width": 3,
     },
   },
+  {
+    selector: 'node.predicted-tm',
+    style: {
+      "border-style": "dashed",
+    },
+  },
   {
     selector: 'node[is_predicted="true"]',
     style: {