diff --git a/README.md b/README.md
index 586a9a6c648015ff769bc2c96fe514ad28278c27..6b3fe1bfb165b7c403f07a3317947a0d36f8bd65 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,7 @@
 
 What does OrthoFinder do?
 ==========
-OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologs, orthogroups, infers gene trees for all orthogroups and infers a species tree for the species being analysed. OrthoFinder also identifies the root of the species tree and provides lots of useful statistics for comparative genomic analyses. OrthoFinder is very simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format .
+OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues, orthogroups, infers gene trees for all orthogroups and infers a species tree for the species being analysed. OrthoFinder also identifies the root of the species tree and provides lots of useful statistics for comparative genomic analyses. OrthoFinder is very simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format .
 
 For more details see the OrthoFinder paper below.
 
diff --git a/Tests/test_orthofinder.py b/Tests/test_orthofinder.py
index a2b9b27179773329e4a70a8ec6790ce9576680a7..66b13aed24cc693382bdb5ed560b6e7a234a1129 100755
--- a/Tests/test_orthofinder.py
+++ b/Tests/test_orthofinder.py
@@ -7,7 +7,6 @@ Created on Wed Dec 16 11:25:10 2015
 """
 
 import os 
-import sys
 import time
 import types
 import datetime
@@ -18,6 +17,7 @@ import filecmp
 import glob
 import random
 import csv
+import argparse
 
 __skipLongTests__ = False
 
@@ -657,28 +657,31 @@ Test to add:
 """  
       
 if __name__ == "__main__":
-    test = None
-    if len(sys.argv) == 1:
-        # run suite
-        suite = unittest.TestLoader().loadTestsFromTestCase(TestCommandLine)
-        unittest.TextTestRunner(verbosity=2).run(suite)
-    else:
-        if len(sys.argv) > 1:
-            if sys.argv[1] == "-binary": 
-                qBinary = True
-                print("Running tests using binary file")
-                if len(sys.argv) > 2:
-                    test = sys.argv[2]
-            else:
-                test = sys.argv[1]  
-        if test == None:
-            suite = unittest.TestLoader().loadTestsFromTestCase(TestCommandLine)
-            unittest.TextTestRunner(verbosity=2).run(suite)
-        else:
-            suite = unittest.TestSuite()
-            suite.addTest(TestCommandLine(test))
-            runner = unittest.TextTestRunner()
-            runner.run(suite)
-
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-b", "--binaries", action="store_true", help="Run tests on binary files")
+    parser.add_argument("-t", "--test", help="Individual test to run")
+    parser.add_argument("-d", "--dir", help="Test program in specified directory")
+    
+    args = parser.parse_args()
+    if args.dir:
+        orthofinder = args.dir + "/orthofinder.py"
+        orthofinder_bin = os.path.splitext(orthofinder)[0]
+        trees_for_orthogroups = args.dir + "/trees_from_MSA.py"
+        trees_for_orthogroups_bin = os.path.splitext(trees_for_orthogroups)[0]
         
+    qBinary = args.binaries
+    print("Testing:")
+    print("  " + orthofinder_bin if qBinary else orthofinder)
+    print("  " + trees_for_orthogroups_bin if qBinary else trees_for_orthogroups)
+    print("")
+    
+    if args.test != None:
+        suite = unittest.TestSuite()
+        print("Running single test: %s" % args.test)
+        suite.addTest(TestCommandLine(args.test))
+        runner = unittest.TextTestRunner()
+        runner.run(suite)
+    else:
+        suite = unittest.TestLoader().loadTestsFromTestCase(TestCommandLine)
+        unittest.TextTestRunner(verbosity=2).run(suite)        
     
diff --git a/orthofinder/__init__.py b/orthofinder/__init__.py
index 120282a02ad8d3d571f675638a0a9ea962579105..ffe9e5c0ac48efaaa1330385a3395857f1591898 100644
--- a/orthofinder/__init__.py
+++ b/orthofinder/__init__.py
@@ -1 +1 @@
-__all__ = ["orthofinder", "scripts"]
+#__all__ = ["orthofinder", "trees_from_MSA", "scripts"]