diff --git a/Utilities/for_taxonomy/get_taxonomy.py b/Utilities/for_taxonomy/get_taxonomy.py
new file mode 100644
index 0000000..4e53028
--- /dev/null
+++ b/Utilities/for_taxonomy/get_taxonomy.py
@@ -0,0 +1,179 @@
+import os
+import sys
+from subprocess import check_output
+from time import sleep
+
+
+output_handle = 'output_taxonomies.csv'
+
+
+def bad_script_call():
+	
+	print('\nPlease input a spreadsheet with ten digit codes in the first column and the genus and species names in the second column. Preferably, the genus and species name will be separated by a space and there will be no extraneous characters in the second column\n\n\tpython get_taxonomy.py --input_file <path to .csv file>\n')
+	exit()
+
+
+def get_args():
+	
+	input_path = ''
+	
+	try:
+		if(sys.argv[1] == '--input_file'):
+			input_path= sys.argv[2]
+		else:
+			bad_script_call()
+	except IndexError:
+		bad_script_call()
+		
+	if(input_path != ''):
+		return input_path
+	else:
+		bad_script_call()
+		
+
+#Deterministic function to return the genus + species name given a line in the input spreadsheet
+def get_name(line):
+	name = line.split(',')[1]
+	if(len(name.split(' ')) > 1):
+		if(name.split(' ')[1].strip() == 'sp' or name.split(' ')[1].strip() == 'sp.'):
+			name = name.split(' ')[0]	
+		else:
+			name = name.split(' ')[0] + ' ' + name.split(' ')[1]
+	elif(len(name.split('_')) > 1):
+		if(name.split('_')[1].strip() == 'sp' or name.split('_')[1].strip() == 'sp.'):
+			name = name.split('_')[0]
+		else:
+			name = name.split('_')[0] + ' ' + name.split('_')[1]
+	elif(len(name.split('-')) > 1):
+		if(name.split('-')[1].strip() == 'sp' or name.split('-')[1].strip() == 'sp.'):
+			name = name.split('-')[0]
+		else:
+			name = name.split('-')[0] + ' ' + name.split('-')[1]
+			
+	return name.split('\n')[0].split('\r')[0].split('(')[0]
+
+
+#Returning all of the genus + species names in the input spreadsheet
+def parse_taxaselection(input_path):
+	taxa = {}
+	for lines in open(input_path, 'r'):
+		for i, line in enumerate(lines.split('\r')):
+			if(len(line.split(',')) > 1 and not ('Clade' in line and 'Taxa' in line)):	
+				taxa.update({ get_name(line) : line.split(',')[0].strip() })
+				
+	return taxa
+	
+
+#This function queries Entrez Search with the genus and species name and returns the taxonomy for each name if available
+def get_taxonomy(taxa):
+	
+	#A rough list of most common clades for reference when multiple taxonomies are returned. Feel free to add to this, just keep the format of the names.
+	clades = { 'op_' : 'opisthokont', 'op_fu_' : 'fung', 'op_me_' : 'metazoa', 'pl_' : 'archaeplastid', 'pl_gr_' : 'green alga', 'pl_rh_' : 'red alga', 'pl_gl_' : 'glaucophyt', 'sr_ap_' : 'apicomplexa', 'sr_ci_' : 'ciliat', 'sr_rh_' : 'rhizari', 'sr_di_' : 'dinoflagell', 'sr_st_' : 'stramenopil', 'ba_' : 'bacteria', 'ba_cy_' : 'cyanobacteria', 'ba_ad_' : 'acidobacteria', 'ba_pa_' : 'alphaproteobacteria', 'ba_pb_' : 'betaproteobacteria', 'ba_pg_' : 'gammaproteobacteria', 'ba_pd' : 'deltaproteobacteria', 'za_' : 'archea', 'ex_' : 'excavata', 'am_' : 'amoeb', 'am_tu_' : 'tubilinea', 'am_di_' : 'discosea', 'op_fb_' : 'fung', 'op_mb_' : 'metazoa', 'pl_rb_' : 'red alga', 'sr_ab_' : 'apicomplexa', 'sr_cb_' : 'ciliat', 'sr_rb_' : 'rhizari', 'sr_db_' : 'dinoflagell', 'sr_sb_' : 'stramenopil', 'am_tb' : 'tubilinea', 'am_db' : 'discosea' }
+
+	taxonomies = {}
+	
+	for taxon in taxa:
+		code = taxa[taxon].lower()
+	
+		print('\nFetching taxonomy for taxon ' + taxon + '\n')
+		try:
+			output = str(check_output('esearch -db taxonomy -query "' + taxon + '" | efetch -format xml', shell = True, executable='/bin/bash'))
+			#sleep(2)
+		
+			taxonomy_strings = []
+			
+			for line in output.split('<'):
+				if('lineage' in line.lower() and 'lineageex' not in line.lower()):
+					if('cellular organisms' in line.split('>')[1].split('\n')[0]):
+						taxonomy_strings.append(line.split('>')[1].split('\n')[0])
+						
+		except:
+			continue
+						
+		
+		
+		hits = 0
+		#If multiple taxonomies were returned
+		if(len(taxonomy_strings) > 1):
+			relevant_taxonomies = []
+			#Check whether the relevant minor clade has a keyword
+			if(code[:6] in clades):
+				keyword = clades[code[:6]]
+				for taxonomy in taxonomy_strings:
+					#Get the taxonomy that contains the keyword
+					if(keyword in taxonomy.lower()):
+						hits += 1
+						relevant_taxonomies.append(taxonomy)
+			#If the minor clade does not have a keyword, check whether the major clade has a keyword
+			elif(code[:3] in clades):
+				keyword = clades[code[:3]]
+				for taxonomy in taxonomy_strings:
+					#Get the taxonomy that contains the keyword
+					if(keyword in taxonomy.lower()):
+						hits += 1
+						relevant_taxonomies.append(taxonomy)
+			else:
+				hits = 2
+				
+			if(hits > 1):
+				final_string = 'MULTIPLE TAXONOMIES: ' + ' | '.join(relevant_taxonomies)
+			else:
+				final_string = relevant_taxonomies[0]
+		elif(len(taxonomy_strings) == 0):
+			final_string = 'NO TAXONOMY RETURNED'
+		else:
+			final_string = taxonomy_strings[0]
+								
+		print(final_string)
+						
+		taxonomies.update({ taxon : final_string })
+    
+	return taxonomies
+	
+
+#Writing the output spreadsheet with taxonomies using the input spreadsheet as a template
+def write_spreadsheet(taxonomies, input_path):
+	
+	with open(output_handle, 'w') as o:
+		for lines in open(input_path, 'r'):
+			for i, line in enumerate(lines.split('\r')):
+				if(len(line.split(',')) > 1 and not ('Clade' in line and 'Taxa' in line)):	
+					if(get_name(line) in taxonomies):
+						line_split = line.strip().split(',')
+						line_split.append(taxonomies[get_name(line)])
+						
+						o.write(','.join(line_split) + '\n')
+					else:
+						o.write(line + '\n')
+			
+
+#This is a one-time-use function to add taxonomy to a specific spreadsheet (R2G and BB counts)
+def add_to_seq_count_spreadsheet():
+
+	used = []
+	
+	with open('seq_counts_taxaselection.csv', 'w') as o:
+		for lines in open(output_handle, 'r'):
+			for count_lines in open('seq_counts_selection.csv', 'r'):
+				for count_line in count_lines.split('\r'):
+					for i, line in enumerate(lines.split('\r')):
+						if(count_line.split(',')[0] in line and count_line.split(',')[0] not in used):
+							used.append(count_line.split(',')[0])
+							o.write(count_line + ',' + line.split(',')[1] + ',' + line.split(',')[6] + '\n')
+    		
+	
+def main():
+
+	input_path = get_args()
+
+	taxa = parse_taxaselection(input_path)
+			
+	taxonomies = get_taxonomy(taxa)
+	
+	write_spreadsheet(taxonomies, input_path)
+	
+	#You will probably never need to use this function
+	#add_to_seq_count_spreadsheet()
+
+	
+main()
\ No newline at end of file