diff --git a/Utilities/for_trees/CountTaxonOccurence.py b/Utilities/for_trees/CountTaxonOccurence.py
index 9022d71..6d169ff 100644
--- a/Utilities/for_trees/CountTaxonOccurence.py
+++ b/Utilities/for_trees/CountTaxonOccurence.py
@@ -5,6 +5,7 @@ Motivation: Count the number of occurrences of each taxa in each OG in a post gu
 Dependencies: Bio python, os, sys
 Inputs: Directory of postguidance files 
 Optional: use the --minor flag and include a file named focal_minors.txt in same folder (do not put file name in command line). This file should be csv of targets (Am_tu, Sr_rh, Sr_ci)
+Optional: OR use the --major flag and include a file named focal_majors.txt in same folder (do not put file name in command line). This file should be csv of targets (Am, Sr)
 Outputs: CSV file tallying all the counts of taxa in each OG file plus minor and major clade tallies
 Command line: python3 CountTaxonOccurence_faster_minor.py  --input <dir of postguidance files> --minor
 '''
@@ -21,8 +22,10 @@ def get_args():
         prog = 'Taxon occurrence counting script',
         description = "Updated June 9, 2024"
     )
+
     parser.add_argument('-i', '--input', type = str, required = True, help = 'Path to the folder containing the aligned/unaligned fasta files')
     parser.add_argument('--minor', action='store_true', help = 'Flag to use focal minor clades from focal_minors.txt')
+    parser.add_argument('--major', action='store_true', help = 'Flag to use focal major clades from focal_majors.txt')
     args = parser.parse_args()
         
     if(args.input.endswith('/')):
@@ -32,10 +35,10 @@ def get_args():
         print('\nThe input folder (--input) could not be found. Make sure you have given the correct path.\n')
         exit()
                 
-    return args.input, args.minor
+    return args.input, args.minor, args.major
 
 
-def count_tips(in_dir, use_focal_minors):
+def count_tips(in_dir, use_focal_minors, use_focal_majors):
     
     focal_minors = []
     if use_focal_minors:
@@ -44,7 +47,17 @@ def count_tips(in_dir, use_focal_minors):
                 focal_minors = f.read().strip().split(',')
                 focal_minors = [minor.strip() for minor in focal_minors]
         except FileNotFoundError:
-            print('A file called focal_minors.txt must be included in the folder with your script. This file should have a csv of target minor clades such as "Am_tu, Sr_ci, Sr_rh"')
+            print('A file called focal_minors.txt must be included. This file should have a csv of target minor clades such as "Am_tu, Sr_ci, Sr_rh"')
+            exit()
+    
+    focal_majors = []
+    if use_focal_majors:
+        try:
+            with open('focal_majors.txt', 'r') as f:
+                focal_majors = f.read().strip().split(',')
+                focal_majors = [major.strip() for major in focal_majors]
+        except FileNotFoundError:
+            print('A file called focal_majors.txt must be included. This file should have a list of target major clades such as "Am, Sr"')
             exit()
     
     count_data = {}
@@ -65,9 +78,11 @@ def count_tips(in_dir, use_focal_minors):
                 major_clade = tip[:2]
                 minor_clade = tip[:5]
                 
-                if use_focal_minors:
-                    if minor_clade not in focal_minors:
-                        continue
+                if use_focal_minors and minor_clade not in focal_minors:
+                    continue
+                
+                if use_focal_majors and major_clade not in focal_majors:
+                    continue
                 
                 major_clades.add(major_clade)
                 minor_clades.add(minor_clade)
@@ -80,6 +95,10 @@ def count_tips(in_dir, use_focal_minors):
         # Filter major and minor clades based on focal minors
         major_clades = sorted({minor[:2] for minor in focal_minors})
         minor_clades = sorted(focal_minors)
+    elif use_focal_majors:
+        # Filter major and minor clades based on focal majors
+        major_clades = sorted(focal_majors)
+        minor_clades = sorted({clade for clade in minor_clades if clade[:2] in focal_majors})
     else:
         major_clades = sorted(major_clades)
         minor_clades = sorted(minor_clades)
@@ -117,8 +136,8 @@ def count_tips(in_dir, use_focal_minors):
 
 
 def main():
-    in_dir, use_focal_minors = get_args()
-    count_tips(in_dir, use_focal_minors)
+    in_dir, use_focal_minors, use_focal_majors = get_args()
+    count_tips(in_dir, use_focal_minors, use_focal_majors)
     
 
 main()