diff --git a/CANDy v2.0.ipynb b/CANDy v2.0.ipynb
index b0b83af..c0bf595 100644
--- a/CANDy v2.0.ipynb	
+++ b/CANDy v2.0.ipynb	
@@ -3890,7 +3890,7 @@
    "id": "1fa04b37",
    "metadata": {},
    "source": [
-    "# MSA: MAFFT"
+    "# MSA: FAMSA"
    ]
   },
   {
@@ -3909,7 +3909,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 79,
+   "execution_count": null,
    "id": "9ceb6174",
    "metadata": {},
    "outputs": [
@@ -8207,30 +8207,30 @@
     }
    ],
    "source": [
-    "#MAFFT\n",
+    "#FAMSA\n",
     "import subprocess\n",
     "from subprocess import Popen, PIPE\n",
     "\n",
-    "def MAFFT(execute = True):\n",
-    "    \"\"\"When execute is True, this function runs the Clustal Omega executable to perform a MSA\"\"\"\n",
+    "def FAMSA(execute = True):\n",
+    "    \"\"\"When execute is True, this function runs the FAMSA executable to perform MSA\"\"\"\n",
     "    if execute: \n",
     "        \n",
-    "        #path to clustalo_exe\n",
-    "        mafft = os.getcwd() + '/mafft' #r\"/Users/winde/Alex/Doctoraat/PyEED/Jupyter Notebooks/mafft\"\n",
+    "        #path to FAMSA executable\n",
+    "        famsa = os.getcwd() + '/famsa'\n",
     "        \n",
     "        #name of the input file\n",
-    "        in_file = os.path.join(jobname, f\"CAZy_{jobname}_inclchar_selected.fasta\") #'/Users/winde/Alex/Doctoraat/PyEED/Jupyter Notebooks/CANDy/V1.0/GH57_All/GH57_MSA_Catdomains_75_cleaned_1.fasta' #s.path.join(jobname, f\"CAZy_{family}_{taxsubset}_{cutoff}_inclchar_selected.fasta\")\n",
+    "        in_file = os.path.join(jobname, f\"CAZy_{jobname}_inclchar_selected.fasta\")\n",
     "\n",
     "        #name you want to give to the outputfile\n",
-    "        out_file = os.path.join(jobname, f\"CAZy_{jobname}_aligned.fasta\") #os.path.join(jobname, f\"CAZy_{family}_{taxsubset}_{cutoff}_aligned.fasta\")\n",
+    "        out_file = os.path.join(jobname, f\"CAZy_{jobname}_aligned.fasta\")\n",
+    "        \n",
+    "        #perform the multiple sequence alignment using FAMSA\n",
+    "        famsa_cmd = [famsa, \"-refine_mode\", \"on\", in_file, out_file]\n",
+    "        p = subprocess.Popen(famsa_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)\n",
+    "        stdout, stderr = p.communicate()\n",
     "        \n",
-    "        #perform the multiple sequence alignment using MAFFT\n",
-    "        mafft_cmd = [\"mafft\", \"--auto\", in_file]\n",
-    "        with open(out_file, \"w\") as outfile:\n",
-    "            p = subprocess.Popen(mafft_cmd, stdout=outfile, stderr=subprocess.PIPE)\n",
-    "            _, error_output = p.communicate()\n",
     "        if p.returncode != 0:\n",
-    "            raise RuntimeError(\"An error occurred while running MAFFT:\\n{}\".format(error_output.decode()))\n",
+    "            raise RuntimeError(\"An error occurred while running FAMSA:\\n{}\".format(stderr.decode()))\n",
     "    \n",
     "        with open(out_file, 'r') as r:\n",
     "            print(r.read())\n",
@@ -8238,7 +8238,7 @@
     "    print('Finished!')\n",
     "    return\n",
     "\n",
-    "alignment = MAFFT(execute)"
+    "alignment = FAMSA(execute)"
    ]
   },
   {
@@ -8265,7 +8265,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 81,
+   "execution_count": null,
    "id": "0cfcbecd",
    "metadata": {},
    "outputs": [
@@ -8279,14 +8279,15 @@
    ],
    "source": [
     "from subprocess import Popen, PIPE\n",
+    "import os\n",
     "\n",
     "def FastTree(execute = True):\n",
-    "    \"\"\"When execute is True, this function runs the FastTree executable to perform PTI\"\"\"\n",
+    "    \"\"\"When execute is True, this function runs the VeryFastTree executable to perform PTI\"\"\"\n",
     "    \n",
     "    if execute:\n",
     "        \n",
-    "        #path to FastTree_exe\n",
-    "        FastTree = os.getcwd() + '/FastTree' #'/Users/winde/Alex/Doctoraat/PyEED/Jupyter Notebooks/FastTree'\n",
+    "        #path to VeryFastTree_exe\n",
+    "        VeryFastTree = os.getcwd() + '/VeryFastTree'\n",
     "        \n",
     "        #name of the inputfile\n",
     "        inputfile = os.path.join(jobname, f\"CAZy_{jobname}_aligned.fasta\") #os.path.join(jobname, f\"CAZy_{family}_{taxsubset}_{cutoff}_aligned.fasta\")\n",
@@ -8294,11 +8295,15 @@
     "        #name of the outputfile\n",
     "        outputfile = os.path.join(jobname, f\"CAZy_{jobname}_phyltree.nwk\") #os.path.join(jobname, f\"CAZy_{family}_{taxsubset}_phyltree.nwk\")\n",
     "        \n",
-    "        #build a phylogenetic tree using FastTree\n",
-    "        fasttree_process = Popen([FastTree, \"-quiet\", \"-out\", outputfile, inputfile], stdout=PIPE, stderr=PIPE)\n",
+    "        # Determine number of CPU cores available and use max - 2\n",
+    "        max_cores = os.cpu_count() or 4  # Default to 4 if cpu_count returns None\n",
+    "        num_threads = max(1, max_cores - 2)  # Ensure at least 1 thread\n",
+    "        \n",
+    "        # Build a phylogenetic tree using VeryFastTree with multithreading\n",
+    "        fasttree_process = Popen([VeryFastTree, \"-threads\", str(num_threads), \"-quiet\", \"-out\", outputfile, inputfile], stdout=PIPE, stderr=PIPE)\n",
     "        stdout, stderr = fasttree_process.communicate()\n",
     "        \n",
-    "        print(f\"{outputfile} finished!\")\n",
+    "        print(f\"{outputfile} finished using {num_threads} threads!\")\n",
     "    \n",
     "    return \n",
     "\n",