diff --git a/Tests/test_orthofinder.py b/Tests/test_orthofinder.py
index a357a684bd41f9cb94af447b7217bb20391903f9..bdc96f77fb4563b10759adc3bd1fea26c905f920 100755
--- a/Tests/test_orthofinder.py
+++ b/Tests/test_orthofinder.py
@@ -32,7 +32,7 @@ exampleBlastDir = baseDir + "Input/SmallExampleDataset_ExampleBlastDir/"
 goldResultsDir_smallExample = baseDir + "ExpectedOutput/SmallExampleDataset/"
 goldPrepareBlastDir = baseDir + "ExpectedOutput/SmallExampleDataset_PreparedForBlast/"
 
-version = "0.7.1"
+version = "1.0.0"
 requiredBlastVersion = "2.2.28+"
 
 citation = """When publishing work that uses OrthoFinder please cite:
diff --git a/scripts/get_orthologues.py b/get_orthologues.py
similarity index 99%
rename from scripts/get_orthologues.py
rename to get_orthologues.py
index f22758c59f832ac2bd83bb8f644856f6fb04da06..61b8e1e8431510578b807671cd2274b9cd9e0cee 100755
--- a/scripts/get_orthologues.py
+++ b/get_orthologues.py
@@ -17,7 +17,7 @@ import itertools
 import multiprocessing as mp
 import Queue
 
-sys.path.append(os.path.split(os.path.abspath(__file__))[0] + "/..")
+#sys.path.append(os.path.split(os.path.abspath(__file__))[0] + "/..")
 import trees_for_orthogroups as tfo
 import orthofinder
 import root_from_duplications as rfd
diff --git a/orthofinder.py b/orthofinder.py
index 5fd08b46088c886b6088b1021637efac759d1e55..b4e72a92576d5135d79d1e3b02aeff8f51762955 100755
--- a/orthofinder.py
+++ b/orthofinder.py
@@ -51,6 +51,7 @@ import Queue                                    # Y
 import warnings                                 # Y
 import time                                     # Y
 
+
 version = "1.0.0"
 fastaExtensions = {"fa", "faa", "fasta", "fas"}
 picProtocol = 1
@@ -1228,7 +1229,6 @@ def AssignIDsToSequences(fastaDirectory, outputDirectory):
     return returnFilenames, originalFastaFilenames, idsFilename, speciesFilename, newSpeciesIDs, previousSpeciesIDs
 
 if __name__ == "__main__":
-    sys.path.append(os.path.split(os.path.abspath(__file__))[0] + "/scripts")
     import get_orthologues
     
     print("\nOrthoFinder version %s Copyright (C) 2014 David Emms\n" % version)
diff --git a/scripts/process_trees.py b/process_trees.py
similarity index 99%
rename from scripts/process_trees.py
rename to process_trees.py
index 94d696b40f1e84360b09d71011861eae4c072be0..1c6c337af88ce75ec5b41fc7e8547518911eac0c 100644
--- a/scripts/process_trees.py
+++ b/process_trees.py
@@ -10,7 +10,6 @@ from ete2 import Tree
 from scipy import sparse
 from collections import defaultdict
 
-sys.path.append(os.path.split(__file__)[0] + "/..")
 import orthofinder 
 
 def natural_sort_key(s, _nsre=re.compile('([0-9]+)')):
@@ -155,4 +154,4 @@ if __name__ == "__main__":
     ogSet = go.OrthoGroupsSet(orthofinderWorkingDir, clustersFilename_pairs, idExtractor = orthofinder.FirstWordExtractor)
     
     get_orthologue_lists(ogSet, resultsDir, dlcparResultsDir, workingDir)
-        
\ No newline at end of file
+        
diff --git a/scripts/root_from_duplications.py b/root_from_duplications.py
similarity index 100%
rename from scripts/root_from_duplications.py
rename to root_from_duplications.py