diff --git a/PanACoTA/__init__.py b/PanACoTA/__init__.py
index 121fd20451e97502656c178ca58963ab2c028651..318e01994a20fd88276abb6d070a971128142caf 100755
--- a/PanACoTA/__init__.py
+++ b/PanACoTA/__init__.py
@@ -1,3 +1,3 @@
 """PanACoTA"""
 
-__version__ = "1.0.1.0"
+__version__ = "1.0.1-2"
diff --git a/PanACoTA/bin/__init__.py b/PanACoTA/bin/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..5980e95b3aade7155ba7f992cf5c15066cb38c46
--- /dev/null
+++ b/PanACoTA/bin/__init__.py
@@ -0,0 +1,31 @@
+# ###############################################################################
+# This file is part of PanACOTA.                                                #
+#                                                                               #
+# Authors: Amandine Perrin                                                      #
+# Copyright © 2018-2020 Institut Pasteur (Paris).                               #
+# See the COPYRIGHT file for details.                                           #
+#                                                                               #
+# PanACOTA is a software providing tools for large scale bacterial comparative  #
+# genomics. From a set of complete and/or draft genomes, you can:               #
+#    -  Do a quality control of your strains, to eliminate poor quality         #
+# genomes, which would not give any information for the comparative study       #
+#    -  Uniformly annotate all genomes                                          #
+#    -  Do a Pan-genome                                                         #
+#    -  Do a Core or Persistent genome                                          #
+#    -  Align all Core/Persistent families                                      #
+#    -  Infer a phylogenetic tree from the Core/Persistent families             #
+#                                                                               #
+# PanACOTA is free software: you can redistribute it and/or modify it under the #
+# terms of the Affero GNU General Public License as published by the Free       #
+# Software Foundation, either version 3 of the License, or (at your option)     #
+# any later version.                                                            #
+#                                                                               #
+# PanACOTA is distributed in the hope that it will be useful, but WITHOUT ANY   #
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS     #
+# FOR A PARTICULAR PURPOSE. See the Affero GNU General Public License           #
+# for more details.                                                             #
+#                                                                               #
+# You should have received a copy of the Affero GNU General Public License      #
+# along with PanACOTA (COPYING file).                                           #
+# If not, see <https://www.gnu.org/licenses/>.                                  #
+# ###############################################################################
diff --git a/bin/PanACoTA b/PanACoTA/bin/run_panacota.py
similarity index 73%
rename from bin/PanACoTA
rename to PanACoTA/bin/run_panacota.py
index 007a25bde0f0c43d046e44661b64eca702975008..a4d3c97271dd9df5aaa83bb10f29fc7fa2e4e867 100755
--- a/bin/PanACoTA
+++ b/PanACoTA/bin/run_panacota.py
@@ -1,6 +1,40 @@
 #!/usr/bin/env python3
 # coding: utf-8
 
+
+# ###############################################################################
+# This file is part of PanACOTA.                                                #
+#                                                                               #
+# Authors: Amandine Perrin                                                      #
+# Copyright © 2018-2020 Institut Pasteur (Paris).                               #
+# See the COPYRIGHT file for details.                                           #
+#                                                                               #
+# PanACOTA is a software providing tools for large scale bacterial comparative  #
+# genomics. From a set of complete and/or draft genomes, you can:               #
+#    -  Do a quality control of your strains, to eliminate poor quality         #
+# genomes, which would not give any information for the comparative study       #
+#    -  Uniformly annotate all genomes                                          #
+#    -  Do a Pan-genome                                                         #
+#    -  Do a Core or Persistent genome                                          #
+#    -  Align all Core/Persistent families                                      #
+#    -  Infer a phylogenetic tree from the Core/Persistent families             #
+#                                                                               #
+# PanACOTA is free software: you can redistribute it and/or modify it under the #
+# terms of the Affero GNU General Public License as published by the Free       #
+# Software Foundation, either version 3 of the License, or (at your option)     #
+# any later version.                                                            #
+#                                                                               #
+# PanACOTA is distributed in the hope that it will be useful, but WITHOUT ANY   #
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS     #
+# FOR A PARTICULAR PURPOSE. See the Affero GNU General Public License           #
+# for more details.                                                             #
+#                                                                               #
+# You should have received a copy of the Affero GNU General Public License      #
+# along with PanACOTA (COPYING file).                                           #
+# If not, see <https://www.gnu.org/licenses/>.                                  #
+# ###############################################################################
+
+
 import sys
 from textwrap import dedent
 
diff --git a/setup.py b/setup.py
index 1d763e24925d3e8a60b61761dfc79bb218fed5cb..ddc049ddcc0d97b047bc6223d455c0c44686ac3f 100755
--- a/setup.py
+++ b/setup.py
@@ -7,13 +7,12 @@ Setup script
 
 import PanACoTA
 try:
-    from setuptools import setup
+    from setuptools import setup, find_packages
     from setuptools.command.test import test as TestCommand
 except ImportError:
-    from distutils.core import setup
+    from distutils.core import setup, find_packages
     from distutils.core import Command as TestCommand
 
-
 class PyTest(TestCommand):
     def initialize_options(self):
         pass
@@ -38,11 +37,11 @@ def parse_requirements(requirements):
                 and not l.startswith('#')]
 
 
-packages = ['PanACoTA', 'PanACoTA.prepare_module', 'PanACoTA.annotate_module',
-            'PanACoTA.pangenome_module', 'PanACoTA.corepers_module',
-            'PanACoTA.align_module', 'PanACoTA.tree_module', 'PanACoTA.subcommands']
+# packages = ['PanACoTA', 'PanACoTA.prepare_module', 'PanACoTA.annotate_module',
+#             'PanACoTA.pangenome_module', 'PanACoTA.corepers_module',
+#             'PanACoTA.align_module', 'PanACoTA.tree_module', 'PanACoTA.subcommands']
 requires = parse_requirements("requirements.txt")
-scripts = ['bin/PanACoTA']
+scripts = ['PanACoTA/bin/run_panacota.py']
 
 classifiers = [
     "Environment :: Console",
@@ -58,7 +57,7 @@ with open('README.md') as f:
 
 setup(
     name='PanACoTA',
-    packages=packages,
+    packages=find_packages(),
     version=PanACoTA.__version__,
     description="Large scale comparative genomics tools: annotate genomes, do pangenome, "
                 "core/persistent genome, align core/persistent families, infer phylogenetic tree.",
@@ -71,8 +70,13 @@ setup(
     package_data={'': ['LICENSE']},
     url='https://github.com/gem-pasteur/PanACoTA',
     scripts=scripts,
+    entry_points={
+          'console_scripts': ['PanACoTA=PanACoTA.bin.run_panacota:main']
+      },
+    python_requires='>=3.4',
     include_package_data=True,
     install_requires=requires,
+    extras_require={'dev': parse_requirements("requirements-dev.txt")},
     tests_require=['pytest'],
     cmdclass={'test': PyTest},
     classifiers=classifiers