Add files to prepare licence

LICENCE-files/avis-licence.txt

+#!/usr/bin/env python3
+# coding: utf-8
+
+###############################################################################
+
+This file is part of PanACOTA.
+
+Authors: Amandine Perrin      
+Copyright © 2016-2018 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/>.
+
+###############################################################################
\ No newline at end of file

LICENCE-files/example-header.txt.md

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+$                                                                                              $
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+$ She alteration everything sympathize impossible his get compliment. Collected                $
+$ few extremity suffering met had sportsman.                                                   $
+$                                                                                              $
+$ Passage its ten led hearted removal cordial. Preference any astonished unreserved            $
+$ mrs. Prosperous understood middletons in conviction an uncommonly do. Supposing              $
+$ so be resolving breakfast am or perfectly. Is drew am hill from mr. Valley by oh twenty      $
+$ direct me so. Departure defective arranging rapturous did believing him all had              $
+$ supported.                                                                                   $
+$ Family months lasted simple se nature vulgar him. Picture fo attempt joy excited             $
+$ ten carried manners talking how. Suspicion neglected he resolving agreement perceived an.    $
+$                                                                                              $
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\ No newline at end of file

LICENCE-files/list-source-files.txt

+genomeAPCAT/__init__.py
+genomeAPCAT/utils.py
+genomeAPCAT/utils_pangenome.py
+genomeAPCAT/align_module/__init__.py
+genomeAPCAT/align_module/alignment.py
+genomeAPCAT/align_module/get_seqs.py
+genomeAPCAT/align_module/pan_to_pergenome.py
+genomeAPCAT/align_module/post_align.py
+genomeAPCAT/annote_module/__init__.py
+genomeAPCAT/annote_module/format_functions.py
+genomeAPCAT/annote_module/genome_seq_functions.py
+genomeAPCAT/annote_module/prokka_functions.py
+genomeAPCAT/corepers_module/__init__.py
+genomeAPCAT/corepers_module/persistent_functions.py
+genomeAPCAT/pangenome_module/__init__.py
+genomeAPCAT/pangenome_module/mmseqs_functions.py
+genomeAPCAT/pangenome_module/post_treatment.py
+genomeAPCAT/pangenome_module/protein_seq_functions.py
+genomeAPCAT/subcommands/__init__.py
+genomeAPCAT/subcommands/align.py
+genomeAPCAT/subcommands/annote.py
+genomeAPCAT/subcommands/corepers.py
+genomeAPCAT/subcommands/pangenome.py
+genomeAPCAT/subcommands/tree.py
+genomeAPCAT/tree_module/__init__.py
+genomeAPCAT/tree_module/fastme_func.py
+genomeAPCAT/tree_module/fasttree_func.py
+genomeAPCAT/tree_module/quicktree_func.py