diff --git a/PanACoTA/subcommands/align.py b/PanACoTA/subcommands/align.py
index 20ec5613ca8016c651d35579c74bc29704a6204f..931e4fc047c3af58a5c7502f7b01ee520799c596 100755
--- a/PanACoTA/subcommands/align.py
+++ b/PanACoTA/subcommands/align.py
@@ -1,6 +1,38 @@
#!/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/>. #
+# ###############################################################################
+
"""
align is a subcommand of PanACoTA
@@ -23,7 +55,7 @@ def main_from_parse(args):
result of argparse parsing of all arguments in command line
"""
cmd = "PanACoTA " + ' '.join(args.argv)
- main(cmd, args.corepers, args.list_genomes, args.dataset_name, args.dbpath,
+ main(cmd, args.corepers, args.list_genomes, args.dataset_name, args.dbpath,
args.outdir, args.threads, args.force, args.verbose, args.quiet)
@@ -99,7 +131,7 @@ def main(cmd, corepers, list_genomes, dname, dbpath, outdir, threads, force, ver
# generate required files
gseqs.get_all_seqs(all_genomes, dname, dbpath, listdir, aldir, fam_nums, quiet)
prefix = os.path.join(aldir, dname)
-
+
# Align all families
status = ali.align_all_families(prefix, fam_nums, len(all_genomes), dname, quiet, threads)
if not status:
diff --git a/PanACoTA/subcommands/annotate.py b/PanACoTA/subcommands/annotate.py
index 54e94539e599a1f7145a72f210512e27f5923939..b406a88f23fa2f9d4cbe8b9a2c08da1455f4d28c 100755
--- a/PanACoTA/subcommands/annotate.py
+++ b/PanACoTA/subcommands/annotate.py
@@ -1,6 +1,38 @@
#!/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/>. #
+# ###############################################################################
+
"""
annotate is a subcommand of PanACoTA
diff --git a/PanACoTA/subcommands/corepers.py b/PanACoTA/subcommands/corepers.py
index ad60a87c626b2830e9118484e7713bcda6b9ac08..8b6db02bf003fbe1d8ccb147dc8d90583a4e2bea 100755
--- a/PanACoTA/subcommands/corepers.py
+++ b/PanACoTA/subcommands/corepers.py
@@ -1,6 +1,38 @@
#!/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/>. #
+# ###############################################################################
+
"""
corepers is a subcommand of PanACoTA
diff --git a/PanACoTA/subcommands/pangenome.py b/PanACoTA/subcommands/pangenome.py
index d52d7c7a1ab5810bcd9c85a1772bb1bdc67ca7ed..202b15e50249127bc308b4dfafee806ddfb67bd9 100755
--- a/PanACoTA/subcommands/pangenome.py
+++ b/PanACoTA/subcommands/pangenome.py
@@ -1,6 +1,38 @@
#!/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/>. #
+# ###############################################################################
+
"""
pangenome is a subcommand of PanACoTA
diff --git a/PanACoTA/subcommands/prepare.py b/PanACoTA/subcommands/prepare.py
index 4079c14ae0b4b6c6cf590d06dda49f78fb4ec9d9..6a9c76591ebd2fa028b85199682e083035531498 100644
--- a/PanACoTA/subcommands/prepare.py
+++ b/PanACoTA/subcommands/prepare.py
@@ -1,6 +1,38 @@
#!/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/>. #
+# ###############################################################################
+
"""
Subcommand to prepare a dataset:
diff --git a/PanACoTA/subcommands/tree.py b/PanACoTA/subcommands/tree.py
index 9ea6e9fb62f28284bcad8ee6f2238b5cc4ae583b..0e7aa5371ad569b493f28ada134a42b1a16224d6 100755
--- a/PanACoTA/subcommands/tree.py
+++ b/PanACoTA/subcommands/tree.py
@@ -1,6 +1,38 @@
#!/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/>. #
+# ###############################################################################
+
"""
tree is a subcommand of PanACoTA